This Python Jupyter notebook counts occurrences of each barcode in each sample from Illumina barcode sequencing, and adds these counts to the codon variant table.
Use plotnine for ggplot2-like plotting.
The analysis relies heavily on the Bloom lab's dms_variants package:
import glob
import itertools
import multiprocessing
import multiprocessing.pool
import os
import warnings
import alignparse
import alignparse.targets
import dms_variants.codonvarianttable
from dms_variants.constants import CBPALETTE
import dms_variants.illuminabarcodeparser
import dms_variants.utils
import dms_variants.plotnine_themes
from IPython.display import display, HTML
import pandas as pd
from plotnine import *
import yamlSet plotnine theme to the gray-grid one defined in dms_variants:
theme_set(dms_variants.plotnine_themes.theme_graygrid())Versions of key software:
print(f"Using alignparse version {alignparse.__version__}")
print(f"Using dms_variants version {dms_variants.__version__}")Using alignparse version 0.2.4
Using dms_variants version 0.8.9
Ignore warnings that clutter output:
warnings.simplefilter('ignore')Read the configuration file:
with open('config.yaml') as f:
config = yaml.safe_load(f)Make output directory if needed:
os.makedirs(config['counts_dir'], exist_ok=True)
os.makedirs(config['figs_dir'], exist_ok=True)Initialize the table of barcode-variant pairs from the respective process_ccs notebooks for each background.
variants = pd.read_csv(config['codon_variant_table_file'], na_filter=None)
display(HTML(variants.head().to_html(index=False)))| target | library | barcode | variant_call_support | codon_substitutions | aa_substitutions | n_codon_substitutions | n_aa_substitutions |
|---|---|---|---|---|---|---|---|
| CGG_naive | lib1 | AAAAAAAAAACACCGG | 6 | GGC119GGT TTA200ACT | L200T | 2 | 1 |
| CGG_naive | lib1 | AAAAAAAAAACATGAG | 1 | CAG16TGG | Q16W | 1 | 1 |
| CGG_naive | lib1 | AAAAAAAAAAGCGACG | 1 | GTG156CAT | V156H | 1 | 1 |
| CGG_naive | lib1 | AAAAAAAAAAGGAAAG | 6 | GTG110GGT | V110G | 1 | 1 |
| CGG_naive | lib1 | AAAAAAAAAATATAGA | 1 | TAC47CCA | Y47P | 1 | 1 |
Pull out a target sequence for matching to the barcode and flanking sequence regions. Note, in this pipeline this is ok because our different backgrounds don't have differing flanks or other features within the actual N16 region covered in Illumina sequencing. If ever placing in-line barcodes here in the future, we would need to modify this.
# get wildtype gene sequence for primary target
targets = alignparse.targets.Targets(seqsfile=config['amplicon'],
feature_parse_specs=config['feature_parse_specs'])Read data frame with list of all barcode runs.
print(f"Reading list of barcode runs from {config['barcode_runs']}")
barcode_runs = (pd.read_csv(config['barcode_runs'])
.assign(R1=lambda x: x['R1'].str.split('; '))
)
display(HTML(barcode_runs.to_html(index=False)))Reading list of barcode runs from data/barcode_runs.csv
| library | sample | sample_type | sort_bin | concentration | date | number_cells | R1 |
|---|---|---|---|---|---|---|---|
| lib1 | SortSeq_bin1 | SortSeq | 1 | NaN | 210621 | 210800 | [/shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib1_bin1-1_S73_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib1_bin1-2_S74_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib1_bin1-3_S75_R1_001.fastq.gz] |
| lib1 | SortSeq_bin2 | SortSeq | 2 | NaN | 210621 | 1984000 | [/shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib1_bin2-1_S76_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib1_bin2-2_S77_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib1_bin2-3_S78_R1_001.fastq.gz] |
| lib1 | SortSeq_bin3 | SortSeq | 3 | NaN | 210621 | 2940000 | [/shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib1_bin3-1_S79_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib1_bin3-2_S80_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib1_bin3_S81_R1_001.fastq.gz] |
| lib1 | SortSeq_bin4 | SortSeq | 4 | NaN | 210621 | 3575000 | [/shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib1_bin4-1_S82_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib1_bin4-2_S83_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib1_bin4-3_S84_R1_001.fastq.gz] |
| lib2 | SortSeq_bin1 | SortSeq | 1 | NaN | 210621 | 275500 | [/shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib2_bin1-1_S85_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib2_bin1-2_S86_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib2_bin1-3_S87_R1_001.fastq.gz] |
| lib2 | SortSeq_bin2 | SortSeq | 2 | NaN | 210621 | 2146000 | [/shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib2_bin2-1_S88_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib2_bin2-2_S89_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib2_bin2-3_S90_R1_001.fastq.gz] |
| lib2 | SortSeq_bin3 | SortSeq | 3 | NaN | 210621 | 2128000 | [/shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib2_bin3-1_S91_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib2_bin3-2_S92_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib2_bin3-3_S93_R1_001.fastq.gz] |
| lib2 | SortSeq_bin4 | SortSeq | 4 | NaN | 210621 | 3850000 | [/shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib2_bin4-1_S94_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib2_bin4-2_S95_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210629_D00300_1271_BHM55FBCX3/Unaligned/Project_tstarr/CGGexpr_lib2_bin4-3_S96_R1_001.fastq.gz] |
| lib1 | PSR_01_bin1 | PSR | 1 | 1.0 | 210623 | 166552 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s1_b1_S1_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s1_b1_S1_R1_001.fastq.gz] |
| lib1 | PSR_01_bin2 | PSR | 2 | 1.0 | 210623 | 1321552 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s1_b2_S2_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s1_b2_S2_R1_001.fastq.gz] |
| lib1 | PSR_01_bin3 | PSR | 3 | 1.0 | 210623 | 2584631 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s1_b3_S3_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s1_b3_S3_R1_001.fastq.gz] |
| lib1 | PSR_01_bin4 | PSR | 4 | 1.0 | 210623 | 1056008 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s1_b4_S4_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s1_b4_S4_R1_001.fastq.gz] |
| lib1 | PSR_02_bin1 | PSR | 1 | 2.0 | 210623 | 226835 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s2_b1_S5_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s2_b1_S5_R1_001.fastq.gz] |
| lib1 | PSR_02_bin2 | PSR | 2 | 2.0 | 210623 | 2109671 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s2_b2_S6_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s2_b2_S6_R1_001.fastq.gz] |
| lib1 | PSR_02_bin3 | PSR | 3 | 2.0 | 210623 | 2116370 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s2_b3_S7_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s2_b3_S7_R1_001.fastq.gz] |
| lib1 | PSR_02_bin4 | PSR | 4 | 2.0 | 210623 | 652024 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s2_b4_S8_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s2_b4_S8_R1_001.fastq.gz] |
| lib1 | PSR_03_bin1 | PSR | 1 | 3.0 | 210623 | 638294 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s3_b1_S9_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s3_b1_S9_R1_001.fastq.gz] |
| lib1 | PSR_03_bin2 | PSR | 2 | 3.0 | 210623 | 2990094 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s3_b2_S10_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s3_b2_S10_R1_001.fastq.gz] |
| lib1 | PSR_03_bin3 | PSR | 3 | 3.0 | 210623 | 1205131 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s3_b3_S11_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s3_b3_S11_R1_001.fastq.gz] |
| lib1 | PSR_03_bin4 | PSR | 4 | 3.0 | 210623 | 328641 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s3_b4_S12_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s3_b4_S12_R1_001.fastq.gz] |
| lib1 | PSR_04_bin1 | PSR | 1 | 4.0 | 210623 | 1810068 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s4_b1_S13_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s4_b1_S13_R1_001.fastq.gz] |
| lib1 | PSR_04_bin2 | PSR | 2 | 4.0 | 210623 | 2620843 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s4_b2_S14_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s4_b2_S14_R1_001.fastq.gz] |
| lib1 | PSR_04_bin3 | PSR | 3 | 4.0 | 210623 | 530641 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s4_b3_S15_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s4_b3_S15_R1_001.fastq.gz] |
| lib1 | PSR_04_bin4 | PSR | 4 | 4.0 | 210623 | 118642 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s4_b4_S16_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s4_b4_S16_R1_001.fastq.gz] |
| lib1 | PSR_05_bin1 | PSR | 1 | 5.0 | 210623 | 4778551 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s5_b1_S17_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s5_b1_S17_R1_001.fastq.gz] |
| lib1 | PSR_05_bin2 | PSR | 2 | 5.0 | 210623 | 353774 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s5_b2_S18_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s5_b2_S18_R1_001.fastq.gz] |
| lib1 | PSR_05_bin3 | PSR | 3 | 5.0 | 210623 | 931 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s5_b3_S19_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s5_b3_S19_R1_001.fastq.gz] |
| lib1 | PSR_05_bin4 | PSR | 4 | 5.0 | 210623 | 86 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib1_s5_b4_S20_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib1_s5_b4_S20_R1_001.fastq.gz] |
| lib2 | PSR_01_bin1 | PSR | 1 | 1.0 | 210623 | 205712 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s1_b1_S21_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s1_b1_S21_R1_001.fastq.gz] |
| lib2 | PSR_01_bin2 | PSR | 2 | 1.0 | 210623 | 1052179 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s1_b2_S22_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s1_b2_S22_R1_001.fastq.gz] |
| lib2 | PSR_01_bin3 | PSR | 3 | 1.0 | 210623 | 2587244 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s1_b3_S23_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s1_b3_S23_R1_001.fastq.gz] |
| lib2 | PSR_01_bin4 | PSR | 4 | 1.0 | 210623 | 1258113 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s1_b4_S24_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s1_b4_S24_R1_001.fastq.gz] |
| lib2 | PSR_02_bin1 | PSR | 1 | 2.0 | 210623 | 92181 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s2_b1_S25_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s2_b1_S25_R1_001.fastq.gz] |
| lib2 | PSR_02_bin2 | PSR | 2 | 2.0 | 210623 | 1595278 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s2_b2_S26_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s2_b2_S26_R1_001.fastq.gz] |
| lib2 | PSR_02_bin3 | PSR | 3 | 2.0 | 210623 | 2631834 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s2_b3_S27_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s2_b3_S27_R1_001.fastq.gz] |
| lib2 | PSR_02_bin4 | PSR | 4 | 2.0 | 210623 | 809181 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s2_b4_S28_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s2_b4_S28_R1_001.fastq.gz] |
| lib2 | PSR_03_bin1 | PSR | 1 | 3.0 | 210623 | 212570 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s3_b1_S29_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s3_b1_S29_R1_001.fastq.gz] |
| lib2 | PSR_03_bin2 | PSR | 2 | 3.0 | 210623 | 2734623 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s3_b2_S30_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s3_b2_S30_R1_001.fastq.gz] |
| lib2 | PSR_03_bin3 | PSR | 3 | 3.0 | 210623 | 2024807 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s3_b3_S31_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s3_b3_S31_R1_001.fastq.gz] |
| lib2 | PSR_03_bin4 | PSR | 4 | 3.0 | 210623 | 394498 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s3_b4_S32_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s3_b4_S32_R1_001.fastq.gz] |
| lib2 | PSR_04_bin1 | PSR | 1 | 4.0 | 210623 | 522992 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s4_b1_S33_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s4_b1_S33_R1_001.fastq.gz] |
| lib2 | PSR_04_bin2 | PSR | 2 | 4.0 | 210623 | 3416342 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s4_b2_S34_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s4_b2_S34_R1_001.fastq.gz] |
| lib2 | PSR_04_bin3 | PSR | 3 | 4.0 | 210623 | 1023529 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s4_b3_S35_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s4_b3_S35_R1_001.fastq.gz] |
| lib2 | PSR_04_bin4 | PSR | 4 | 4.0 | 210623 | 137633 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s4_b4_S36_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s4_b4_S36_R1_001.fastq.gz] |
| lib2 | PSR_05_bin1 | PSR | 1 | 5.0 | 210623 | 4937652 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s5_b1_S37_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s5_b1_S37_R1_001.fastq.gz] |
| lib2 | PSR_05_bin2 | PSR | 2 | 5.0 | 210623 | 852436 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s5_b2_S38_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s5_b2_S38_R1_001.fastq.gz] |
| lib2 | PSR_05_bin3 | PSR | 3 | 5.0 | 210623 | 1912 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s5_b3_S39_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s5_b3_S39_R1_001.fastq.gz] |
| lib2 | PSR_05_bin4 | PSR | 4 | 5.0 | 210623 | 123 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/PSR_lib2_s5_b4_S40_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/PSR_lib2_s5_b4_S40_R1_001.fastq.gz] |
| lib1 | TiteSeq_01_bin1 | TiteSeq | 1 | 1.0 | 210624 | 9967 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s01-b1_S53_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s01-b1_S53_R1_001.fastq.gz] |
| lib1 | TiteSeq_01_bin2 | TiteSeq | 2 | 1.0 | 210624 | 100694 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s01-b2_S54_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s01-b2_S54_R1_001.fastq.gz] |
| lib1 | TiteSeq_01_bin3 | TiteSeq | 3 | 1.0 | 210624 | 910229 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s01-b3_S55_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s01-b3_S55_R1_001.fastq.gz] |
| lib1 | TiteSeq_01_bin4 | TiteSeq | 4 | 1.0 | 210624 | 4152079 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s01-b4_S56_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s01-b4_S56_R1_001.fastq.gz] |
| lib1 | TiteSeq_02_bin1 | TiteSeq | 1 | 2.0 | 210624 | 78772 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s02-b1_S57_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s02-b1_S57_R1_001.fastq.gz] |
| lib1 | TiteSeq_02_bin2 | TiteSeq | 2 | 2.0 | 210624 | 363643 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s02-b2_S58_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s02-b2_S58_R1_001.fastq.gz] |
| lib1 | TiteSeq_02_bin3 | TiteSeq | 3 | 2.0 | 210624 | 1099977 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s02-b3_S59_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s02-b3_S59_R1_001.fastq.gz] |
| lib1 | TiteSeq_02_bin4 | TiteSeq | 4 | 2.0 | 210624 | 3597621 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s02-b4_S60_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s02-b4_S60_R1_001.fastq.gz] |
| lib1 | TiteSeq_03_bin1 | TiteSeq | 1 | 3.0 | 210624 | 165484 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s03-b1_S61_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s03-b1_S61_R1_001.fastq.gz] |
| lib1 | TiteSeq_03_bin2 | TiteSeq | 2 | 3.0 | 210624 | 563920 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s03-b2_S62_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s03-b2_S62_R1_001.fastq.gz] |
| lib1 | TiteSeq_03_bin3 | TiteSeq | 3 | 3.0 | 210624 | 1517930 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s03-b3_S63_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s03-b3_S63_R1_001.fastq.gz] |
| lib1 | TiteSeq_03_bin4 | TiteSeq | 4 | 3.0 | 210624 | 2863005 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s03-b4_S64_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s03-b4_S64_R1_001.fastq.gz] |
| lib1 | TiteSeq_04_bin1 | TiteSeq | 1 | 4.0 | 210624 | 292375 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s04-b1_S65_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s04-b1_S65_R1_001.fastq.gz] |
| lib1 | TiteSeq_04_bin2 | TiteSeq | 2 | 4.0 | 210624 | 715622 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s04-b2_S66_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s04-b2_S66_R1_001.fastq.gz] |
| lib1 | TiteSeq_04_bin3 | TiteSeq | 3 | 4.0 | 210624 | 2461781 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s04-b3_S67_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s04-b3_S67_R1_001.fastq.gz] |
| lib1 | TiteSeq_04_bin4 | TiteSeq | 4 | 4.0 | 210624 | 1745862 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s04-b4_S68_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s04-b4_S68_R1_001.fastq.gz] |
| lib1 | TiteSeq_05_bin1 | TiteSeq | 1 | 5.0 | 210624 | 410552 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s05-b1_S69_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s05-b1_S69_R1_001.fastq.gz] |
| lib1 | TiteSeq_05_bin2 | TiteSeq | 2 | 5.0 | 210624 | 1513776 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s05-b2_S70_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s05-b2_S70_R1_001.fastq.gz] |
| lib1 | TiteSeq_05_bin3 | TiteSeq | 3 | 5.0 | 210624 | 3204858 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s05-b3_S71_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s05-b3_S71_R1_001.fastq.gz] |
| lib1 | TiteSeq_05_bin4 | TiteSeq | 4 | 5.0 | 210624 | 48951 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s05-b4_S72_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s05-b4_S72_R1_001.fastq.gz] |
| lib1 | TiteSeq_06_bin1 | TiteSeq | 1 | 6.0 | 210624 | 1352339 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s06-b1_S73_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s06-b1_S73_R1_001.fastq.gz] |
| lib1 | TiteSeq_06_bin2 | TiteSeq | 2 | 6.0 | 210624 | 3598153 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s06-b2_S74_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s06-b2_S74_R1_001.fastq.gz] |
| lib1 | TiteSeq_06_bin3 | TiteSeq | 3 | 6.0 | 210624 | 98238 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s06-b3_S75_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s06-b3_S75_R1_001.fastq.gz] |
| lib1 | TiteSeq_06_bin4 | TiteSeq | 4 | 6.0 | 210624 | 17 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s06-b4_S76_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s06-b4_S76_R1_001.fastq.gz] |
| lib1 | TiteSeq_07_bin1 | TiteSeq | 1 | 7.0 | 210624 | 4214830 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s07-b1_S77_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s07-b1_S77_R1_001.fastq.gz] |
| lib1 | TiteSeq_07_bin2 | TiteSeq | 2 | 7.0 | 210624 | 814937 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s07-b2_S78_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s07-b2_S78_R1_001.fastq.gz] |
| lib1 | TiteSeq_07_bin3 | TiteSeq | 3 | 7.0 | 210624 | 321 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s07-b3_S79_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s07-b3_S79_R1_001.fastq.gz] |
| lib1 | TiteSeq_07_bin4 | TiteSeq | 4 | 7.0 | 210624 | 4 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s07-b4_S80_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s07-b4_S80_R1_001.fastq.gz] |
| lib1 | TiteSeq_08_bin1 | TiteSeq | 1 | 8.0 | 210624 | 4879499 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s08-b1_S81_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s08-b1_S81_R1_001.fastq.gz] |
| lib1 | TiteSeq_08_bin2 | TiteSeq | 2 | 8.0 | 210624 | 166605 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s08-b2_S82_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s08-b2_S82_R1_001.fastq.gz] |
| lib1 | TiteSeq_08_bin3 | TiteSeq | 3 | 8.0 | 210624 | 110 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s08-b3_S83_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s08-b3_S83_R1_001.fastq.gz] |
| lib1 | TiteSeq_08_bin4 | TiteSeq | 4 | 8.0 | 210624 | 34 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s08-b4_S84_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s08-b4_S84_R1_001.fastq.gz] |
| lib1 | TiteSeq_09_bin1 | TiteSeq | 1 | 9.0 | 210624 | 4994518 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s09-b1_S85_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s09-b1_S85_R1_001.fastq.gz] |
| lib1 | TiteSeq_09_bin2 | TiteSeq | 2 | 9.0 | 210624 | 97766 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s09-b2_S86_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s09-b2_S86_R1_001.fastq.gz] |
| lib1 | TiteSeq_09_bin3 | TiteSeq | 3 | 9.0 | 210624 | 156 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s09-b3_S87_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s09-b3_S87_R1_001.fastq.gz] |
| lib1 | TiteSeq_09_bin4 | TiteSeq | 4 | 9.0 | 210624 | 57 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s09-b4_S88_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s09-b4_S88_R1_001.fastq.gz] |
| lib2 | TiteSeq_01_bin1 | TiteSeq | 1 | 1.0 | 210624 | 5023 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s10-b1_S89_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s10-b1_S89_R1_001.fastq.gz] |
| lib2 | TiteSeq_01_bin2 | TiteSeq | 2 | 1.0 | 210624 | 85666 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s10-b2_S90_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s10-b2_S90_R1_001.fastq.gz] |
| lib2 | TiteSeq_01_bin3 | TiteSeq | 3 | 1.0 | 210624 | 910355 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s10-b3_S91_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s10-b3_S91_R1_001.fastq.gz] |
| lib2 | TiteSeq_01_bin4 | TiteSeq | 4 | 1.0 | 210624 | 4087566 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s10-b4_S92_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s10-b4_S92_R1_001.fastq.gz] |
| lib2 | TiteSeq_02_bin1 | TiteSeq | 1 | 2.0 | 210624 | 64354 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s11-b1_S93_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s11-b1_S93_R1_001.fastq.gz] |
| lib2 | TiteSeq_02_bin2 | TiteSeq | 2 | 2.0 | 210624 | 377819 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s11-b2_S94_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s11-b2_S94_R1_001.fastq.gz] |
| lib2 | TiteSeq_02_bin3 | TiteSeq | 3 | 2.0 | 210624 | 1149394 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s11-b3_S95_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s11-b3_S95_R1_001.fastq.gz] |
| lib2 | TiteSeq_02_bin4 | TiteSeq | 4 | 2.0 | 210624 | 3595640 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s11-b4_S96_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s11-b4_S96_R1_001.fastq.gz] |
| lib2 | TiteSeq_03_bin1 | TiteSeq | 1 | 3.0 | 210624 | 146993 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s12-b1_S97_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s12-b1_S97_R1_001.fastq.gz] |
| lib2 | TiteSeq_03_bin2 | TiteSeq | 2 | 3.0 | 210624 | 585863 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s12-b2_S98_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s12-b2_S98_R1_001.fastq.gz] |
| lib2 | TiteSeq_03_bin3 | TiteSeq | 3 | 3.0 | 210624 | 1546007 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s12-b3_S99_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s12-b3_S99_R1_001.fastq.gz] |
| lib2 | TiteSeq_03_bin4 | TiteSeq | 4 | 3.0 | 210624 | 2888203 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s12-b4_S100_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s12-b4_S100_R1_001.fastq.gz] |
| lib2 | TiteSeq_04_bin1 | TiteSeq | 1 | 4.0 | 210624 | 229759 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s13-b1_S101_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s13-b1_S101_R1_001.fastq.gz] |
| lib2 | TiteSeq_04_bin2 | TiteSeq | 2 | 4.0 | 210624 | 754199 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s13-b2_S102_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s13-b2_S102_R1_001.fastq.gz] |
| lib2 | TiteSeq_04_bin3 | TiteSeq | 3 | 4.0 | 210624 | 2383948 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s13-b3_S103_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s13-b3_S103_R1_001.fastq.gz] |
| lib2 | TiteSeq_04_bin4 | TiteSeq | 4 | 4.0 | 210624 | 1851348 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s13-b4_S104_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s13-b4_S104_R1_001.fastq.gz] |
| lib2 | TiteSeq_05_bin1 | TiteSeq | 1 | 5.0 | 210624 | 330918 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s14-b1_S105_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s14-b1_S105_R1_001.fastq.gz] |
| lib2 | TiteSeq_05_bin2 | TiteSeq | 2 | 5.0 | 210624 | 1498361 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s14-b2_S106_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s14-b2_S106_R1_001.fastq.gz] |
| lib2 | TiteSeq_05_bin3 | TiteSeq | 3 | 5.0 | 210624 | 3161208 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s14-b3_S107_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s14-b3_S107_R1_001.fastq.gz] |
| lib2 | TiteSeq_05_bin4 | TiteSeq | 4 | 5.0 | 210624 | 54642 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s14-b4_S108_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s14-b4_S108_R1_001.fastq.gz] |
| lib2 | TiteSeq_06_bin1 | TiteSeq | 1 | 6.0 | 210624 | 1260056 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s15-b1_S109_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s15-b1_S109_R1_001.fastq.gz] |
| lib2 | TiteSeq_06_bin2 | TiteSeq | 2 | 6.0 | 210624 | 3701958 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s15-b2_S110_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s15-b2_S110_R1_001.fastq.gz] |
| lib2 | TiteSeq_06_bin3 | TiteSeq | 3 | 6.0 | 210624 | 90277 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s15-b3_S111_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s15-b3_S111_R1_001.fastq.gz] |
| lib2 | TiteSeq_06_bin4 | TiteSeq | 4 | 6.0 | 210624 | 19 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s15-b4_S112_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s15-b4_S112_R1_001.fastq.gz] |
| lib2 | TiteSeq_07_bin1 | TiteSeq | 1 | 7.0 | 210624 | 4182689 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s16-b1_S41_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s16-b1_S41_R1_001.fastq.gz] |
| lib2 | TiteSeq_07_bin2 | TiteSeq | 2 | 7.0 | 210624 | 830786 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s16-b2_S42_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s16-b2_S42_R1_001.fastq.gz] |
| lib2 | TiteSeq_07_bin3 | TiteSeq | 3 | 7.0 | 210624 | 273 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s26-b3_S43_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s26-b3_S43_R1_001.fastq.gz] |
| lib2 | TiteSeq_07_bin4 | TiteSeq | 4 | 7.0 | 210624 | 20 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s16-b4_S44_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s16-b4_S44_R1_001.fastq.gz] |
| lib2 | TiteSeq_08_bin1 | TiteSeq | 1 | 8.0 | 210624 | 4893728 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s17-b1_S45_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s17-b1_S45_R1_001.fastq.gz] |
| lib2 | TiteSeq_08_bin2 | TiteSeq | 2 | 8.0 | 210624 | 154510 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s17-b2_S46_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s17-b2_S46_R1_001.fastq.gz] |
| lib2 | TiteSeq_08_bin3 | TiteSeq | 3 | 8.0 | 210624 | 83 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s17-b3_S47_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s17-b3_S47_R1_001.fastq.gz] |
| lib2 | TiteSeq_08_bin4 | TiteSeq | 4 | 8.0 | 210624 | 23 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s17-b4_S48_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s17-b4_S48_R1_001.fastq.gz] |
| lib2 | TiteSeq_09_bin1 | TiteSeq | 1 | 9.0 | 210624 | 5016672 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s18-b1_S49_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s18-b1_S49_R1_001.fastq.gz] |
| lib2 | TiteSeq_09_bin2 | TiteSeq | 2 | 9.0 | 210624 | 86684 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s18-b2_S50_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s18-b2_S50_R1_001.fastq.gz] |
| lib2 | TiteSeq_09_bin3 | TiteSeq | 3 | 9.0 | 210624 | 50 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s18-b3_S51_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s18-b3_S51_R1_001.fastq.gz] |
| lib2 | TiteSeq_09_bin4 | TiteSeq | 4 | 9.0 | 210624 | 3 | [/shared/ngs/illumina/tstarr/210728_D00300_1288_AHMGMTBCX3/Unaligned/Project_tstarr/210624_s18-b4_S52_R1_001.fastq.gz, /shared/ngs/illumina/tstarr/210701_D00300_1272_BHM532BCX3/Unaligned/Project_tstarr/210624_s18-b4_S52_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_01_bin1 | TuGG_TiteSeq | 1 | 1.0 | 210624 | 95588 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s01-b1_S1_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_01_bin2 | TuGG_TiteSeq | 2 | 1.0 | 210624 | 4168050 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s01-b2_S2_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_01_bin3 | TuGG_TiteSeq | 3 | 1.0 | 210624 | 4184690 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s01-b3_S3_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_01_bin4 | TuGG_TiteSeq | 4 | 1.0 | 210624 | 1183718 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s01-b4_S4_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_02_bin1 | TuGG_TiteSeq | 1 | 2.0 | 210624 | 3314375 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s02-b1_S5_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_02_bin2 | TuGG_TiteSeq | 2 | 2.0 | 210624 | 5019870 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s02-b2_S6_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_02_bin3 | TuGG_TiteSeq | 3 | 2.0 | 210624 | 648425 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s02-b3_S7_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_02_bin4 | TuGG_TiteSeq | 4 | 2.0 | 210624 | 157814 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s02-b4_S8_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_03_bin1 | TuGG_TiteSeq | 1 | 3.0 | 210624 | 3125305 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s03-b1_S9_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_03_bin2 | TuGG_TiteSeq | 2 | 3.0 | 210624 | 5256079 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s03-b2_S10_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_03_bin3 | TuGG_TiteSeq | 3 | 3.0 | 210624 | 953327 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s03-b3_S11_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_03_bin4 | TuGG_TiteSeq | 4 | 3.0 | 210624 | 120068 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s03-b4_S12_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_04_bin1 | TuGG_TiteSeq | 1 | 4.0 | 210624 | 7469770 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s04-b1_S13_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_04_bin2 | TuGG_TiteSeq | 2 | 4.0 | 210624 | 760060 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s04-b2_S14_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_04_bin3 | TuGG_TiteSeq | 3 | 4.0 | 210624 | 36335 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s04-b3_S15_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_04_bin4 | TuGG_TiteSeq | 4 | 4.0 | 210624 | 17293 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s04-b4_S16_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_05_bin1 | TuGG_TiteSeq | 1 | 5.0 | 210624 | 6294823 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s05-b1_S17_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_05_bin2 | TuGG_TiteSeq | 2 | 5.0 | 210624 | 151581 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s05-b2_S18_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_05_bin3 | TuGG_TiteSeq | 3 | 5.0 | 210624 | 3155 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s05-b3_S19_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_05_bin4 | TuGG_TiteSeq | 4 | 5.0 | 210624 | 1286 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s05-b4_S20_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_06_bin1 | TuGG_TiteSeq | 1 | 6.0 | 210624 | 8590833 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s06-b1_S21_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_06_bin2 | TuGG_TiteSeq | 2 | 6.0 | 210624 | 180075 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s06-b2_S22_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_06_bin3 | TuGG_TiteSeq | 3 | 6.0 | 210624 | 2343 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s06-b3_S23_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_06_bin4 | TuGG_TiteSeq | 4 | 6.0 | 210624 | 912 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s06-b4_S24_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_07_bin1 | TuGG_TiteSeq | 1 | 7.0 | 210624 | 8613053 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s07-b1_S25_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_07_bin2 | TuGG_TiteSeq | 2 | 7.0 | 210624 | 186532 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s07-b2_S26_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_07_bin3 | TuGG_TiteSeq | 3 | 7.0 | 210624 | 690 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s07-b3_S27_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_07_bin4 | TuGG_TiteSeq | 4 | 7.0 | 210624 | 684 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s07-b4_S28_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_09_bin1 | TuGG_TiteSeq | 1 | 9.0 | 210624 | 8975223 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s09-b1_S29_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_09_bin2 | TuGG_TiteSeq | 2 | 9.0 | 210624 | 268793 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s09-b2_S30_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_09_bin3 | TuGG_TiteSeq | 3 | 9.0 | 210624 | 697 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s09-b3_S31_R1_001.fastq.gz] |
| lib1 | TuGG_TiteSeq_09_bin4 | TuGG_TiteSeq | 4 | 9.0 | 210624 | 727 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s09-b4_S32_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_01_bin1 | TuGG_TiteSeq | 1 | 1.0 | 210624 | 115152 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s10-b1_S33_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_01_bin2 | TuGG_TiteSeq | 2 | 1.0 | 210624 | 5524687 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s10-b2_S34_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_01_bin3 | TuGG_TiteSeq | 3 | 1.0 | 210624 | 3023595 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s10-b3_S35_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_01_bin4 | TuGG_TiteSeq | 4 | 1.0 | 210624 | 669346 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s10-b4_S36_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_02_bin1 | TuGG_TiteSeq | 1 | 2.0 | 210624 | 3655690 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s11-b1_S37_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_02_bin2 | TuGG_TiteSeq | 2 | 2.0 | 210624 | 5318467 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s11-b2_S38_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_02_bin3 | TuGG_TiteSeq | 3 | 2.0 | 210624 | 484880 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s11-b3_S39_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_02_bin4 | TuGG_TiteSeq | 4 | 2.0 | 210624 | 136565 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s11-b4_S40_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_03_bin1 | TuGG_TiteSeq | 1 | 3.0 | 210624 | 2973732 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s12-b1_S41_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_03_bin2 | TuGG_TiteSeq | 2 | 3.0 | 210624 | 5603928 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s12-b2_S42_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_03_bin3 | TuGG_TiteSeq | 3 | 3.0 | 210624 | 830237 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s12-b3_S43_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_03_bin4 | TuGG_TiteSeq | 4 | 3.0 | 210624 | 77414 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s12-b4_S44_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_04_bin1 | TuGG_TiteSeq | 1 | 4.0 | 210624 | 9411050 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s13-b1_S45_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_04_bin2 | TuGG_TiteSeq | 2 | 4.0 | 210624 | 868830 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s13-b2_S46_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_04_bin3 | TuGG_TiteSeq | 3 | 4.0 | 210624 | 24669 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s13-b3_S47_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_04_bin4 | TuGG_TiteSeq | 4 | 4.0 | 210624 | 15997 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s13-b4_S48_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_05_bin1 | TuGG_TiteSeq | 1 | 5.0 | 210624 | 9099859 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s14-b1_S49_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_05_bin2 | TuGG_TiteSeq | 2 | 5.0 | 210624 | 230472 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s14-b2_S50_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_05_bin3 | TuGG_TiteSeq | 3 | 5.0 | 210624 | 12450 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s14-b3_S51_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_05_bin4 | TuGG_TiteSeq | 4 | 5.0 | 210624 | 5709 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s14-b4_S52_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_06_bin1 | TuGG_TiteSeq | 1 | 6.0 | 210624 | 9243226 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s15-b1_S53_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_06_bin2 | TuGG_TiteSeq | 2 | 6.0 | 210624 | 207411 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s15-b2_S54_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_06_bin3 | TuGG_TiteSeq | 3 | 6.0 | 210624 | 4539 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s15-b3_S55_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_06_bin4 | TuGG_TiteSeq | 4 | 6.0 | 210624 | 1069 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s15-b4_S56_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_07_bin1 | TuGG_TiteSeq | 1 | 7.0 | 210624 | 9230106 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s16-b1_S57_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_07_bin2 | TuGG_TiteSeq | 2 | 7.0 | 210624 | 177944 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s16-b2_S58_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_07_bin3 | TuGG_TiteSeq | 3 | 7.0 | 210624 | 502 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s16-b3_S59_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_07_bin4 | TuGG_TiteSeq | 4 | 7.0 | 210624 | 684 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s16-b4_S60_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_09_bin1 | TuGG_TiteSeq | 1 | 9.0 | 210624 | 9196329 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s18-b1_S61_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_09_bin2 | TuGG_TiteSeq | 2 | 9.0 | 210624 | 279088 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s18-b2_S62_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_09_bin3 | TuGG_TiteSeq | 3 | 9.0 | 210624 | 618 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s18-b3_S63_R1_001.fastq.gz] |
| lib2 | TuGG_TiteSeq_09_bin4 | TuGG_TiteSeq | 4 | 9.0 | 210624 | 731 | [/shared/ngs/illumina/tstarr/220428_VH00699_111_AAATNWKM5/Unaligned/Project_tstarr/220420_s18-b4_S64_R1_001.fastq.gz] |
Make sure library / sample combinations are unique:
assert len(barcode_runs) == len(barcode_runs.groupby(['library', 'sample']))Make sure the the libraries for which we have barcode runs are all in our variant table:
unknown_libs = set(barcode_runs['library']) - set(variants['library'])
if unknown_libs:
raise ValueError(f"Libraries with barcode runs not in variant table: {unknown_libs}")Now we initialize an IlluminaBarcodeParser for each library.
First, get the length of the barcode from the alignment target after making sure the same length for all targets:
bclen = len(targets.targets[0].get_feature('barcode').seq)
assert (bclen == len(target.get_feature('barcode').seq) for target in targets.targets)
print(f"Barcodes of length {bclen}")Barcodes of length 16
The other barcode parsing params come from the config file:
parser_params = config['illumina_barcode_parser_params']
display(HTML(
pd.Series(parser_params, name='value')
.rename_axis(index='parameter')
.reset_index()
.to_html(index=False)
))| parameter | value |
|---|---|
| upstream | GGCCGC |
| downstream | |
| minq | 20 |
| upstream_mismatch | 1 |
| downstream_mismatch | 0 |
The parser needs to know the set of valid barcodes, which are stored in the variant table and are different for each library. So we create a different parser for each library using these valid barcode sets:
# create dict keyed by library, value is parser for library
parsers = {lib: dms_variants.illuminabarcodeparser.IlluminaBarcodeParser(
bclen=bclen,
valid_barcodes=variants.loc[variants['library']==lib]['barcode'],
**parser_params)
for lib in set(variants['library'])}
print('Number of valid barcodes searched for by each parser:')
display(HTML(
pd.DataFrame([(lib, len(p.valid_barcodes)) for lib, p in parsers.items()],
columns=['library', 'number of valid barcodes'])
.to_html(index=False)
))Number of valid barcodes searched for by each parser:
| library | number of valid barcodes |
|---|---|
| lib2 | 99370 |
| lib1 | 93059 |
We now parse the barcodes.
Since this will take a while, we utilize multiple CPUs via the Python multiprocessing module.
First, determine how many CPUs to use.
We use the minimum of the user-specified number hardcoded below and the number actually available.
(If you are running interactively on the Hutch cluster, you may need to reduce the number below in order to avoid an error as there is an enforced CPU limit on the home rhino nodes):
ncpus = min(config['max_cpus'], multiprocessing.cpu_count())
print(f"Using {ncpus} CPUs")Using 8 CPUs
Parse the barcodes in parallel via a multiprocessing.Pool using all the available CPUs to get a list of the data frames with barcode counts / fates for each sample:
def process_func(parser, r1files, library, sample):
"""Convenience function to be starmapped to multiprocessing pool."""
return parser.parse(r1files, add_cols={'library': library, 'sample': sample})
# parallel computation of list of data frames
with multiprocessing.pool.Pool(processes=ncpus) as pool:
bclist = pool.starmap(
process_func,
[(parsers[run.library], run.R1, run.library, run.sample)
for run in barcode_runs.itertuples()],
)Now concatenate the list into data frames of barcode counts and barcode fates:
counts = pd.concat([samplecounts for samplecounts, _ in bclist],
sort=False,
ignore_index=True)
print('First few lines of counts data frame:')
display(HTML(counts.head().to_html(index=False)))
fates = pd.concat([samplefates for _, samplefates in bclist],
sort=False,
ignore_index=True)
print('First few lines of fates data frame:')
display(HTML(fates.head().to_html(index=False)))First few lines of counts data frame:
| barcode | count | library | sample |
|---|---|---|---|
| AGCATACCCTTAACAA | 26343 | lib1 | SortSeq_bin1 |
| TGACGCCTTATCCTCC | 20015 | lib1 | SortSeq_bin1 |
| TGCGATGGTACGTCAA | 15678 | lib1 | SortSeq_bin1 |
| AACTACACGGATAGGT | 14906 | lib1 | SortSeq_bin1 |
| CATAATGAATGTGCAA | 14667 | lib1 | SortSeq_bin1 |
First few lines of fates data frame:
| fate | count | library | sample |
|---|---|---|---|
| valid barcode | 5878929 | lib1 | SortSeq_bin1 |
| invalid barcode | 4760919 | lib1 | SortSeq_bin1 |
| low quality barcode | 833191 | lib1 | SortSeq_bin1 |
| failed chastity filter | 523889 | lib1 | SortSeq_bin1 |
| unparseable barcode | 144412 | lib1 | SortSeq_bin1 |
First, we'll analyze the "fates" of the parsed barcodes. These fates represent what happened to each Illumina read we parsed:
- Did the barcode read fail the Illumina chastity filter?
- Was the barcode unparseable (i.e., the read didn't appear to be a valid barcode based on flanking regions)?
- Was the barcode sequence too low quality based on the Illumina quality scores?
- Was the barcode parseable but invalid (i.e., not in our list of variant-associated barcodes in the codon variant table)?
- Was the barcode valid, and so will be added to variant counts.
First, we just write a CSV file with all the barcode fates:
fatesfile = os.path.join(config['counts_dir'], 'barcode_fates.csv')
print(f"Writing barcode fates to {fatesfile}")
fates.to_csv(fatesfile, index=False)Writing barcode fates to results/counts/barcode_fates.csv
Next, we tabulate the barcode fates in wide format:
display(HTML(fates
.pivot_table(columns='fate',
values='count',
index=['library', 'sample'])
.to_html()
))| fate | failed chastity filter | invalid barcode | low quality barcode | unparseable barcode | valid barcode | |
|---|---|---|---|---|---|---|
| library | sample | |||||
| lib1 | PSR_01_bin1 | 2760 | 76609 | 8875 | 6707 | 261892 |
| PSR_01_bin2 | 33281 | 881110 | 105293 | 53648 | 3071392 | |
| PSR_01_bin3 | 92962 | 2527624 | 304416 | 138579 | 8713391 | |
| PSR_01_bin4 | 31565 | 876540 | 105307 | 43313 | 2878818 | |
| PSR_02_bin1 | 2260 | 60269 | 7086 | 6288 | 213345 | |
| PSR_02_bin2 | 54573 | 1384490 | 182158 | 79424 | 4816497 | |
| PSR_02_bin3 | 53449 | 1521122 | 179420 | 83758 | 5160624 | |
| PSR_02_bin4 | 20733 | 573716 | 65237 | 35128 | 1834236 | |
| PSR_03_bin1 | 9640 | 265342 | 33949 | 17255 | 925723 | |
| PSR_03_bin2 | 105581 | 2853238 | 337705 | 155594 | 9923513 | |
| PSR_03_bin3 | 37799 | 1031692 | 125139 | 60195 | 3437962 | |
| PSR_03_bin4 | 8856 | 240557 | 28232 | 17746 | 784493 | |
| PSR_04_bin1 | 59868 | 1541305 | 186597 | 87915 | 5366232 | |
| PSR_04_bin2 | 85427 | 2272152 | 275607 | 124985 | 7832291 | |
| PSR_04_bin3 | 16986 | 468779 | 54832 | 24042 | 1546298 | |
| PSR_04_bin4 | 2689 | 63613 | 7695 | 4497 | 204246 | |
| PSR_05_bin1 | 96819 | 2602487 | 315146 | 136049 | 8845215 | |
| PSR_05_bin2 | 4712 | 111266 | 13496 | 9240 | 374768 | |
| PSR_05_bin3 | 945 | 25681 | 2129 | 3216 | 59291 | |
| PSR_05_bin4 | 170 | 216 | 11 | 2451 | 307 | |
| SortSeq_bin1 | 523889 | 4760919 | 833191 | 144412 | 5878929 | |
| SortSeq_bin2 | 727426 | 3538326 | 1173192 | 251148 | 11430301 | |
| SortSeq_bin3 | 746488 | 3531818 | 1201586 | 256451 | 11931433 | |
| SortSeq_bin4 | 699173 | 3195131 | 1123721 | 237730 | 11077972 | |
| TiteSeq_01_bin1 | 723 | 23498 | 2512 | 5588 | 69967 | |
| TiteSeq_01_bin2 | 2219 | 66911 | 7438 | 5391 | 211761 | |
| TiteSeq_01_bin3 | 27109 | 736192 | 89164 | 35800 | 2428144 | |
| TiteSeq_01_bin4 | 109822 | 2886347 | 371062 | 153582 | 9840677 | |
| TiteSeq_02_bin1 | 529 | 15276 | 1740 | 2432 | 47643 | |
| TiteSeq_02_bin2 | 5857 | 157481 | 19898 | 12004 | 527511 | |
| TiteSeq_02_bin3 | 29469 | 836629 | 98832 | 53673 | 2724171 | |
| TiteSeq_02_bin4 | 118649 | 3200851 | 390447 | 198223 | 10962044 | |
| TiteSeq_03_bin1 | 3000 | 85774 | 10330 | 7465 | 281796 | |
| TiteSeq_03_bin2 | 15854 | 439081 | 51347 | 24883 | 1432261 | |
| TiteSeq_03_bin3 | 39990 | 1079409 | 133347 | 66266 | 3548895 | |
| TiteSeq_03_bin4 | 87944 | 2313093 | 290636 | 145619 | 7918255 | |
| TiteSeq_04_bin1 | 4473 | 119291 | 13553 | 9937 | 391594 | |
| TiteSeq_04_bin2 | 12230 | 336998 | 39710 | 17381 | 1104003 | |
| TiteSeq_04_bin3 | 79614 | 2132495 | 262375 | 117650 | 7168931 | |
| TiteSeq_04_bin4 | 33025 | 756991 | 106613 | 42706 | 2610429 | |
| TiteSeq_05_bin1 | 6038 | 166913 | 19351 | 8995 | 551036 | |
| TiteSeq_05_bin2 | 14001 | 388159 | 44619 | 26975 | 1282207 | |
| TiteSeq_05_bin3 | 43395 | 1115507 | 137192 | 66894 | 3825622 | |
| TiteSeq_05_bin4 | 2961 | 82456 | 8955 | 10805 | 254728 | |
| TiteSeq_06_bin1 | 16330 | 478179 | 56630 | 24360 | 1588020 | |
| TiteSeq_06_bin2 | 115068 | 2983159 | 367642 | 162896 | 10241861 | |
| TiteSeq_06_bin3 | 3482 | 102260 | 11895 | 6229 | 341369 | |
| TiteSeq_06_bin4 | 281 | 3381 | 415 | 4784 | 11254 | |
| TiteSeq_07_bin1 | 105301 | 2712156 | 342585 | 147733 | 9198668 | |
| TiteSeq_07_bin2 | 12495 | 340544 | 41258 | 27318 | 1167631 | |
| TiteSeq_07_bin3 | 32 | 752 | 62 | 362 | 1381 | |
| TiteSeq_07_bin4 | 22 | 66 | 7 | 405 | 170 | |
| TiteSeq_08_bin1 | 21561 | 558221 | 70630 | 29815 | 1894494 | |
| TiteSeq_08_bin2 | 2670 | 59900 | 7131 | 8911 | 205514 | |
| TiteSeq_08_bin3 | 59 | 186 | 24 | 1876 | 152 | |
| TiteSeq_08_bin4 | 54 | 530 | 30 | 875 | 99 | |
| TiteSeq_09_bin1 | 119463 | 3152051 | 390186 | 167576 | 10674684 | |
| TiteSeq_09_bin2 | 1161 | 28927 | 3801 | 3064 | 101073 | |
| TiteSeq_09_bin3 | 297 | 212 | 30 | 2671 | 245 | |
| TiteSeq_09_bin4 | 24 | 33 | 3 | 623 | 38 | |
| TuGG_TiteSeq_01_bin1 | 0 | 34391 | 23747 | 1961 | 116108 | |
| TuGG_TiteSeq_01_bin2 | 0 | 1922364 | 1364144 | 101478 | 6630549 | |
| TuGG_TiteSeq_01_bin3 | 0 | 2196495 | 1579084 | 116910 | 7395863 | |
| TuGG_TiteSeq_01_bin4 | 0 | 585227 | 413973 | 26731 | 1890834 | |
| TuGG_TiteSeq_02_bin1 | 0 | 1614297 | 1137941 | 87986 | 5526837 | |
| TuGG_TiteSeq_02_bin2 | 0 | 2565247 | 1801977 | 136491 | 8702674 | |
| TuGG_TiteSeq_02_bin3 | 0 | 349017 | 230950 | 14592 | 1144828 | |
| TuGG_TiteSeq_02_bin4 | 0 | 115817 | 75467 | 4357 | 360140 | |
| TuGG_TiteSeq_03_bin1 | 0 | 1889580 | 1339872 | 100000 | 6449176 | |
| TuGG_TiteSeq_03_bin2 | 0 | 3134038 | 2267255 | 167143 | 10700456 | |
| TuGG_TiteSeq_03_bin3 | 0 | 555265 | 377589 | 24604 | 1769918 | |
| TuGG_TiteSeq_03_bin4 | 0 | 76135 | 50551 | 3004 | 241069 | |
| TuGG_TiteSeq_04_bin1 | 0 | 4128786 | 3065871 | 218040 | 13962133 | |
| TuGG_TiteSeq_04_bin2 | 0 | 441448 | 323055 | 22549 | 1492240 | |
| TuGG_TiteSeq_04_bin3 | 0 | 30016 | 23203 | 1640 | 99049 | |
| TuGG_TiteSeq_04_bin4 | 0 | 10838 | 10579 | 493 | 33093 | |
| TuGG_TiteSeq_05_bin1 | 0 | 3555675 | 2560495 | 182995 | 11997496 | |
| TuGG_TiteSeq_05_bin2 | 0 | 114228 | 81702 | 5314 | 385899 | |
| TuGG_TiteSeq_05_bin3 | 0 | 1740 | 1489 | 83 | 4804 | |
| TuGG_TiteSeq_05_bin4 | 0 | 1702 | 3115 | 122 | 5965 | |
| TuGG_TiteSeq_06_bin1 | 0 | 5006492 | 3662674 | 262476 | 16875795 | |
| TuGG_TiteSeq_06_bin2 | 0 | 107709 | 78938 | 5455 | 371868 | |
| TuGG_TiteSeq_06_bin3 | 0 | 820 | 5824 | 56 | 2002 | |
| TuGG_TiteSeq_06_bin4 | 0 | 2139 | 794 | 31 | 2644 | |
| TuGG_TiteSeq_07_bin1 | 0 | 4294140 | 3141335 | 223749 | 14519467 | |
| TuGG_TiteSeq_07_bin2 | 0 | 138356 | 99278 | 7064 | 468326 | |
| TuGG_TiteSeq_07_bin3 | 0 | 145 | 687 | 10 | 460 | |
| TuGG_TiteSeq_07_bin4 | 0 | 853 | 1125 | 30 | 2244 | |
| TuGG_TiteSeq_09_bin1 | 0 | 4624113 | 3273253 | 239292 | 15612776 | |
| TuGG_TiteSeq_09_bin2 | 0 | 138172 | 101697 | 6871 | 461580 | |
| TuGG_TiteSeq_09_bin3 | 0 | 159 | 270 | 7 | 363 | |
| TuGG_TiteSeq_09_bin4 | 0 | 2682 | 726 | 48 | 347 | |
| lib2 | PSR_01_bin1 | 1562 | 48082 | 5022 | 2414 | 142422 |
| PSR_01_bin2 | 20497 | 602681 | 65954 | 28390 | 1808361 | |
| PSR_01_bin3 | 86014 | 2634986 | 278379 | 127365 | 7845102 | |
| PSR_01_bin4 | 42006 | 1312985 | 139987 | 67516 | 3798485 | |
| PSR_02_bin1 | 1367 | 42002 | 4283 | 2837 | 123214 | |
| PSR_02_bin2 | 36368 | 1058378 | 117892 | 55020 | 3164506 | |
| PSR_02_bin3 | 46831 | 1418500 | 157480 | 68029 | 4240036 | |
| PSR_02_bin4 | 15274 | 471859 | 50349 | 20475 | 1341122 | |
| PSR_03_bin1 | 1207 | 36838 | 3683 | 2161 | 108908 | |
| PSR_03_bin2 | 16676 | 482083 | 51289 | 29575 | 1455089 | |
| PSR_03_bin3 | 42131 | 1353775 | 138689 | 65531 | 4013190 | |
| PSR_03_bin4 | 3981 | 129208 | 12911 | 6491 | 364997 | |
| PSR_04_bin1 | 4946 | 159115 | 16241 | 8762 | 480145 | |
| PSR_04_bin2 | 26313 | 823098 | 87697 | 41658 | 2460338 | |
| PSR_04_bin3 | 34705 | 1027936 | 108936 | 52602 | 3013980 | |
| PSR_04_bin4 | 4733 | 143584 | 15200 | 7153 | 409592 | |
| PSR_05_bin1 | 161760 | 4804606 | 525383 | 228965 | 14207135 | |
| PSR_05_bin2 | 24225 | 720718 | 80451 | 35555 | 2143354 | |
| PSR_05_bin3 | 218 | 4214 | 417 | 1597 | 12272 | |
| PSR_05_bin4 | 39 | 54 | 3 | 1003 | 69 | |
| SortSeq_bin1 | 509852 | 4627673 | 813556 | 198130 | 5774217 | |
| SortSeq_bin2 | 795781 | 4205255 | 1267242 | 273376 | 11874774 | |
| SortSeq_bin3 | 821118 | 4127023 | 1307794 | 275945 | 12092240 | |
| SortSeq_bin4 | 759644 | 3827605 | 1201061 | 262920 | 11482708 | |
| TiteSeq_01_bin1 | 127 | 1831 | 94 | 1012 | 1607 | |
| TiteSeq_01_bin2 | 1683 | 60948 | 5501 | 2139 | 138650 | |
| TiteSeq_01_bin3 | 20885 | 623761 | 65554 | 26992 | 1727022 | |
| TiteSeq_01_bin4 | 61074 | 1710486 | 197991 | 82328 | 5071442 | |
| TiteSeq_02_bin1 | 1144 | 40401 | 3776 | 2800 | 98705 | |
| TiteSeq_02_bin2 | 1702 | 56116 | 5737 | 3198 | 153481 | |
| TiteSeq_02_bin3 | 15466 | 510137 | 51261 | 23383 | 1453815 | |
| TiteSeq_02_bin4 | 73472 | 2044968 | 243880 | 102647 | 6077556 | |
| TiteSeq_03_bin1 | 3090 | 99733 | 9989 | 4813 | 252931 | |
| TiteSeq_03_bin2 | 5054 | 178199 | 17369 | 8192 | 472019 | |
| TiteSeq_03_bin3 | 31150 | 981385 | 103120 | 50095 | 2791190 | |
| TiteSeq_03_bin4 | 72237 | 2133857 | 239146 | 111556 | 6424338 | |
| TiteSeq_04_bin1 | 4149 | 131597 | 12881 | 7011 | 350326 | |
| TiteSeq_04_bin2 | 9666 | 317245 | 32646 | 15224 | 890010 | |
| TiteSeq_04_bin3 | 29876 | 994115 | 104818 | 53698 | 2885157 | |
| TiteSeq_04_bin4 | 23366 | 772506 | 82782 | 40686 | 2355943 | |
| TiteSeq_05_bin1 | 4485 | 149378 | 15427 | 7103 | 410521 | |
| TiteSeq_05_bin2 | 15788 | 493051 | 50774 | 31407 | 1385127 | |
| TiteSeq_05_bin3 | 43332 | 1452937 | 160151 | 75502 | 4361933 | |
| TiteSeq_05_bin4 | 1896 | 53281 | 5713 | 6059 | 164249 | |
| TiteSeq_06_bin1 | 19487 | 644683 | 66729 | 30172 | 1798422 | |
| TiteSeq_06_bin2 | 95814 | 2818095 | 321691 | 144996 | 8444622 | |
| TiteSeq_06_bin3 | 1435 | 44191 | 4834 | 5635 | 138017 | |
| TiteSeq_06_bin4 | 156 | 97 | 11 | 3070 | 80 | |
| TiteSeq_07_bin1 | 65227 | 1880842 | 212932 | 89992 | 5545021 | |
| TiteSeq_07_bin2 | 7847 | 236386 | 25683 | 12951 | 717704 | |
| TiteSeq_07_bin3 | 453 | 10530 | 1149 | 1273 | 31884 | |
| TiteSeq_07_bin4 | 84 | 18 | 15 | 1004 | 20 | |
| TiteSeq_08_bin1 | 92740 | 2822029 | 313287 | 134308 | 8350688 | |
| TiteSeq_08_bin2 | 4522 | 115452 | 11996 | 18720 | 341937 | |
| TiteSeq_08_bin3 | 119 | 87 | 2 | 6303 | 84 | |
| TiteSeq_08_bin4 | 214 | 76 | 12 | 2888 | 204 | |
| TiteSeq_09_bin1 | 89791 | 2691236 | 296258 | 133990 | 7891843 | |
| TiteSeq_09_bin2 | 1902 | 59097 | 5963 | 4419 | 172182 | |
| TiteSeq_09_bin3 | 33 | 18 | 7 | 554 | 12 | |
| TiteSeq_09_bin4 | 94 | 41 | 12 | 2863 | 28 | |
| TuGG_TiteSeq_01_bin1 | 0 | 31702 | 23044 | 1543 | 92273 | |
| TuGG_TiteSeq_01_bin2 | 0 | 3162590 | 2048929 | 152791 | 9480848 | |
| TuGG_TiteSeq_01_bin3 | 0 | 1769269 | 1123222 | 82113 | 5198219 | |
| TuGG_TiteSeq_01_bin4 | 0 | 393281 | 237384 | 16229 | 1065719 | |
| TuGG_TiteSeq_02_bin1 | 0 | 2032170 | 1305656 | 95452 | 6032770 | |
| TuGG_TiteSeq_02_bin2 | 0 | 3133119 | 1999689 | 148307 | 9247875 | |
| TuGG_TiteSeq_02_bin3 | 0 | 322132 | 196005 | 13757 | 882369 | |
| TuGG_TiteSeq_02_bin4 | 0 | 90093 | 54537 | 3178 | 242549 | |
| TuGG_TiteSeq_03_bin1 | 0 | 1651110 | 1099708 | 81919 | 4915217 | |
| TuGG_TiteSeq_03_bin2 | 0 | 3413796 | 2190110 | 161361 | 10112490 | |
| TuGG_TiteSeq_03_bin3 | 0 | 517845 | 316503 | 22759 | 1444008 | |
| TuGG_TiteSeq_03_bin4 | 0 | 51487 | 31545 | 2061 | 137134 | |
| TuGG_TiteSeq_04_bin1 | 0 | 6091206 | 3896498 | 291082 | 17920346 | |
| TuGG_TiteSeq_04_bin2 | 0 | 505427 | 325386 | 23879 | 1478934 | |
| TuGG_TiteSeq_04_bin3 | 0 | 18101 | 11433 | 717 | 48966 | |
| TuGG_TiteSeq_04_bin4 | 0 | 12022 | 7406 | 351 | 32557 | |
| TuGG_TiteSeq_05_bin1 | 0 | 5215279 | 3353563 | 241708 | 15314750 | |
| TuGG_TiteSeq_05_bin2 | 0 | 133936 | 87198 | 5853 | 389948 | |
| TuGG_TiteSeq_05_bin3 | 0 | 4027 | 2955 | 132 | 11063 | |
| TuGG_TiteSeq_05_bin4 | 0 | 1032 | 942 | 34 | 2826 | |
| TuGG_TiteSeq_06_bin1 | 0 | 5127003 | 3332522 | 238833 | 15016308 | |
| TuGG_TiteSeq_06_bin2 | 0 | 123626 | 80514 | 5773 | 368137 | |
| TuGG_TiteSeq_06_bin3 | 0 | 507 | 1630 | 112 | 907 | |
| TuGG_TiteSeq_06_bin4 | 0 | 7564 | 1356 | 92 | 786 | |
| TuGG_TiteSeq_07_bin1 | 0 | 5387435 | 3457670 | 251249 | 15872663 | |
| TuGG_TiteSeq_07_bin2 | 0 | 91426 | 59985 | 4501 | 274519 | |
| TuGG_TiteSeq_07_bin3 | 0 | 48 | 481 | 22 | 82 | |
| TuGG_TiteSeq_07_bin4 | 0 | 247 | 220 | 14 | 578 | |
| TuGG_TiteSeq_09_bin1 | 0 | 5152250 | 3377972 | 237627 | 15119369 | |
| TuGG_TiteSeq_09_bin2 | 0 | 137924 | 89875 | 6420 | 406898 | |
| TuGG_TiteSeq_09_bin3 | 0 | 105 | 997 | 9 | 194 | |
| TuGG_TiteSeq_09_bin4 | 0 | 407 | 260 | 29 | 1008 |
Now we plot the barcode-read fates for each library / sample, showing the bars for valid barcodes in orange and the others in gray. We see that the largest fraction of barcode reads correspond to valid barcodes, and most of the others are invalid barcodes (probably because the map to variants that aren't present in our variant table since we didn't associate all variants with barcodes). The exception to this is lib2 Titeseq_03_bin3; the PCR for this sample in the original sequencing run failed, so we followed it up with a single MiSeq lane. We did not filter out the PhiX reads from this data before parsing, so these PhiX reads will deflate the fraction of valid barcode reads as expected, but does not indicate any problems.
barcode_fate_plot = (
ggplot(
fates
.assign(sample=lambda x: pd.Categorical(x['sample'],
x['sample'].unique(),
ordered=True),
fate=lambda x: pd.Categorical(x['fate'],
x['fate'].unique(),
ordered=True),
is_valid=lambda x: x['fate'] == 'valid barcode'
),
aes('fate', 'count', fill='is_valid')) +
geom_bar(stat='identity') +
facet_grid('sample ~ library') +
facet_grid('sample ~ library') +
scale_fill_manual(CBPALETTE, guide=False) +
theme(figure_size=(1.4 * (1 + fates['library'].nunique()),
1.7 * (1.2 + fates['sample'].nunique())),
axis_text_x=element_text(angle=90),
panel_grid_major_x=element_blank()
) +
scale_y_continuous(labels=dms_variants.utils.latex_sci_not,
name='number of reads')
)
_ = barcode_fate_plot.draw()
print(f"Writing variant counts to {config['variant_counts_file']}")
counts.to_csv(config['variant_counts_file'], index=False)Writing variant counts to results/counts/variant_counts.csv
The CodonVariantTable has lots of nice functions that can be used to analyze the counts it contains. However, we do that in the next notebook so we don't have to re-run this entire (rather computationally intensive) notebook every time we want to analyze a new aspect of the counts.