- Table of contents
- User guide
- Update log
- Copyright
Welcome to phasihunter 😉
A multithreaded program for mining phasiRNA regulation pathways based on multiple reference sequences.
phasihunter is a CLI program runing on linux platform. The correction runing of phasihunter depends on some existing softwares.
- Bowtie (Langmead, et al., 2009. Genome Biol)
- Biopython (Cock, et al., 2009. Bioinformatics)
- Bedtools (Quinlan and Hall, 2010. Bioinformatics)
- Dnapi (Tsuji and Weng, 2016. PloS One)
- Trim_galore (https://github.com/FelixKrueger/TrimGalore)
- Seqkit (Shen, et al., 2016. PloS One)
- Perl5 (https://www.perl.org)
- Fasta36 (Pearson and Lipman, 1988. Proc Natl Acad Sci U S A)
- TarHunter (Ma, et al., 2018. Bioinformatics)
-
Install all dependencies
-
Clone phasihunter
git clone https://github.com/HuangLab-CBI/PhasiHunter.git . -
Setting enviroment variable in ~/.bashrc
echo "export PATH=\$PATH:<phasihunter PATH> >> ~/.bashrc"example:
echo "export PATH=\$PATH:/home/user/volumes/PhasiHunter >> ~/.bashrc" -
type
phasihunter -hto check phasihunter whether installation correct. If phasiHunter is installed correctly you will see the following content.
For convenience, we also provide a Docker image at https://hub.docker.com/repository/docker/zacksfeng/phasihunter
The Docker image has been configured with all the dependencies required for running phasiHunter.
We also provide a conda/mamba environment configuration file. User can install all the required dependencies with command conda/mamba create -f /foo/PhasiHunter/bin/env.yaml
Download link
https://cbi.njau.edu.cn/PhasiHunter_demo_data/test_osa.tar.gz
Parameter in < > means necessary; parameter in [ ] means optional
- Data pre-process
phasiHunter preprocess -m r -i /home/user/test_osa/SRR5049781.fastq.gz -mi 19 -ma 25 -e 1 -n 1000000 -o /home/user/test_osa/SRR5049781_processed_cdna.map -in /home/user/test_osa/index/oryza_sativa_cdna_index
phasiHunter preprocess -m m -i /home/user/test_osa/SRR5049781_trimmed_format_filter.fa -mi 19 -ma 25 -e 1 -n 1000000 -o /home/user/test_osa/SRR5049781_processed_gdna.map -in /home/user/test_osa/index/oryza_sativa_gdna_index- preprocess module usage
Help messeage:
options:
# necessary options:
-m: string -- mode: r | c | m;
raw(mode): trim adaptor --> normalization --> length and abundance filter --> mapping
clean(mode): normalization --> length and abundance filter --> mapping
mapping(mode): mapping
-i: file -- for r mode: fastq file or fastq.gz file
for c mode: fasta file or fasta.gz file
for m mode: length and abundance filter fasta file
-r: file -- reference sequence fasta file
-in: string -- index prefix, -r option will be ignored when -in enable
-o: outfile -- outfile name
# options with default value
-j: int -- adaptor trim parallel cores; <8 is recommend, only need in r mode, default=1
-bj: int -- bowtie parallel cores; defalut=1
-mh: int -- max hits when mapping to ref sequence, default=10
-mi: int -- minimal sRNA reads length cutoff, default=19
-ma: int -- maxmial sRNA reads length cutoff, default=25
-e: float -- sRNA reads cpm cutoff, default=1
-n: int -- normalization base, default=1000000
# other
-v: -- print version information
-h: -- print help information- PhasiRNA and PHAS loci prediction
phasiHunter phase -cm /home/user/test_osa/SRR5049781_processed_cdna.map -c /home/user/test_osa/oryza_sativa_cdna.fa -gm /home/user/test_osa/SRR5049781_processed_gdna.map -g /home/user/test_osa/oryza_sativa_gdna.fa -fm None -f None -fa /home/user/test_osa/SRR5049781_trimmed_format_filter.fa -a /home/user/test_osa/phase_a.txt -o /home/user/test_osa/phase_o.txt -me b -il 5 -pl 21 -pn 4 -mh 10 -j 20 -pv 0.001 -ps 15 -pr 0.4 -cl y- phase module usage
phase usage:
option:
-cm: file -- map file based on reference transcriptome sequence
-c: file -- reference transcritome sequence, fasta file
-gm: file -- map file based on reference genome sequence
-g: file -- reference genome sequence, fasta file
-fm: file -- map file based on full length transcriptome sequence
-f: file -- full length transcriptome sequence, fasta file
-fa: file -- sRNA file
-a: out -- allsiRNA cluster output file, default name is phase_a.txt
-o: out -- phasiRNA cluster output file, default name is phase_o.txt
-me: str -- phasiRNA prediction method, h(hypergeometric test) | p(phase score) | b (both), default=b
-il: int -- phasiRNA cluster island, default=5
-pl: int -- phase length, 21 | 24, default=21
-pn: int -- phase number, default=4
-mh: int -- max hits when mapping to ref sequence, default=10
-j: int -- parallel number, default=1
-pv: float -- pvalue cutoff, default=0.001, only function with h/b method applied
-ps: float -- phase score cutoff, default=15, only function with p/b method applied
-pr: float -- phase ratio cutoff, default=0.4, only function with p/b method applied
-cl: str -- delete .phasiHuter_bowtieIndex, y|n, default=y
-v: -- print version information
-h: -- print help information- PhasiRNA and PHAS loci result integration
phasiHunter integration -io /home/user/test_osa/phase_o.txt -ia /home/user/test_osa/phase_a.txt -an /home/user/test_osa/oryza_sativa_gdna.gff3 -g y -o /home/user/test_osa/integration_o.txt -a /home/user/test_osa/integration_a.txt -s /home/user/test_osa/integration_s.txt -po /home/user/test_osa/integration_p.txt -j 1 -pn 4 -pl 21 -pv 0.001 -il 5- integration module usage
integration usage:
option:
# necessary options:
-io: file -- phase module -o output file
-ia: file -- phase module -a output file
-an: file -- reference genome gff3 file
-g: str -- y | n, whether exist gdna based PHAS Loci
# options with default value
-o: out -- integration phasiRNA cluster, default name is integration_o.txt
-a: out -- integration all siRNA cluster, default name is integration_a.txt
-s: out -- integration summary, default name is integration_s.txt
-po: out -- PHAS Loci information, default name is integration_p.txt
-j: int -- parallel number, default=1
-pn: int -- phase number, default=4
-pl: int -- phase length, 21 | 24, default=21
-pv: float -- pvalue cutoff, default=0.001
-il: int -- phasiRNA cluster island, default=5
-dp: str -- y | n, discard only P method result, default=y
# optional options
-fn: file -- full length transcript annotation file
# other
-v: -- print version information
-h: -- print help information- Print phasiRNA_cluster plot, phasiRNA.fa, PHAS.fa
phasiHunter visulization -io /home/user/test_osa/integration_o.txt -ia /home/user/test_osa/integration_a.txt -ip /home/user/test_osa/integration_p.txt -a /home/user/test_osa/alignment.txt -o /home/user/test_osa/phasiRNA.fa -p /home/user/test_osa/PHAS.fa -pl 21 -m 10 -c /home/user/test_osa/oryza_sativa_cdna.fa -g /home/user/test_osa/oryza_sativa_gdna.fa -f None -pc y -pg y -pf n- visulization module usage
visulization usage:
option:
# necessary options:
-io: file -- integration -io outputfile
-ia: file -- integration -ia outputfile
-ip: file -- integration -po outputfile
-a: out -- alignment file, default name is alignment.txt
-o: out -- phasiRNA fasta file, default name is phasiRNA.fa
-p: out -- PHAS Gene fasta file; Format: >geneid/chr\tphasiRNA_cluster_region(start end)\tseq_region(start end), default name is PHAS.fa
# options with default value
-pl: int -- phase length, 21 | 24, default=21
-m: float -- the number for reducing the size of Y-axis. default=10
# optional options
-c: file -- reference transcritome sequence, fasta file, enable cdna based phasiRNA.fa, PHAS.fa, Alignmen, Plot output
-g: file -- reference genome sequence, fasta file, enable gdna based phasiRNA.fa, PHAS.fa, Alignmen, Plot output
-f: file -- full length transcriptome sequence, fasta file, enable flnc based phasiRNA.fa, PHAS.fa, Alignmen, Plot output
-pc: str -- plot cdna based phasiRNA cluster, y | n, defaut=y
-pg: str -- plot gdna based phasiRNA cluster, y | n, defaut=y
-pf: str -- plot flnc based phasiRNA cluster, y | n, defaut=y
# other
-v: -- print version information
-h: -- print help information- Initiator prediction and verification
phasiHunter target -q /home/user/test_osa/osa.miRbase.fa -b /home/user/test_osa/PHAS.fa -o /home/user/test_osa/miR_target.txt -T 10
phasiHunter initiator -i /home/user/test_osa/integration_o.txt -j /home/user/test_osa/miR_target.txt -ip /home/user/test_osa/integration_p.txt -pd 5 -pl 21 -ps 1 -o /home/user/test_osa/initiator.txt
phasiHunter deg -i /home/user/test_osa/deg/GSM1040649_format_filter.map -q /home/user/test_osa/osa.miRbase.fa -j /home/user/test_osa/initiator.txt -t /home/user/test_osa/oryza_sativa_cdna.fa -o GSM1040649_MTI_deg.txt -s 1 -m 0 -p y -in y -pl 1 -pf MTI_deg --lib GSM1040649 -less- target module usage
Usage:
perl /home/user/volumes/PhasiHunter/bin/TarHunterL_Modified.pl -q <mir_file> -b <targ_file> -o <out_file> [Options]
Required arguments:
-q (--qmir): query miRNA file
-b (--targ): target file
-o (--output): output file
Options:
-M (--total_misp): max. total mispairs [Default: off]
-m (--seed_misp): max. seed mispairs [Default: off]
-f (--score): score cutoff [Default: 4 ]
-I (--mimics): eTM search [Default: off]
-i (--mimics_str): eTM stringency
(0: strict, 1: relaxed) [Default: 0 ]
-T (--threads): FASTA threads [Default: 1 ]
-t (--tab): tabular format output [Default: off]
-h (--help): help information
Dependencies:
fasta36 - initiator module usage
initiator option:
-i [str]integration -o output
-j [str]the target predicted by psRNAtarget server or target module
-ip [str]integration -po output
-pd [int]the microRNA distance away to phase border, default=105(21) or 120 (24), optional
-pl [int]21 or 24, the phase length of 21 or 24, default=21
-ps [int]0 or 1, the position of cleavage at 10(0) or 9-11 (1), default=1
-o [str]outputfilename.
-h print the version and details of the usage- deg module usage
// function: vertified the sRNA - Target interaction with degradome data
options:
-i: <inputfilename> -- mapping file for degradome data mapping transcripts, by bowtie
-q: <sRNA fasta> -- small RNA sequences used for target prediction, fasta
-j: <inputfilename> -- from psRNATarget batch download file or initiator output
-t: <inputfilename> -- transcripts file, fasta
-o: <outputfilename> -- matched map file with only matched records
-s: <shift_number> -- if shifts=0 then cleaved exactly at pos.10, default=1
-m: <minum deg_num> -- minum number of degradome reads, int, default=0
-p: <T-plot function> -- enable the plot function, y | n, default='n'
-in: <bool> -- y | n, use initiator output information
-pl [int] -- 1,plot only category 1; 2, plot categories 1 and 2, default=1
-pf [str] -- output folder name, for exporting t-plot images and outputfile
--lib [str] -- library name
-less -- only output cat_1 and cat_2 information
***********************
//About the categories:
Cat #1, degradome read at the cleavage site is most abundant.
Cat #2, the read is less than the most abudant one, but higher than the median.
Cat #3, the read is less than the median, but high than 1
Cat #4, the read is identical or less than 1 (if degradome data is normalized)- PhasiRNA target prediction and verification
phasiHunter target -q /home/user/test_osa/phasiRNA.fa -b /home/user/test_osa/oryza_sativa_cdna.fa -o /home/user/test_osa/phasiRNA_target.txt -T 10
phasiHunter deg -i /home/user/test_osa/deg/GSM1040649_format_filter.map -q /home/user/test_osa/phasiRNA.fa -j /home/user/test_osa/phasiRNA_target.txt -t /home/user/test_osa/oryza_sativa_cdna.fa -o GSM1040649_PTI_deg.txt -s 1 -m 0 -p y -in n -pl 1 -pf PTI_deg --lib GSM1040649 -lessOne-command module usage
One command executing mode
Usage:
phasiHunter run [-i] [config file]
phasiHunter run -d
option:
-i: yaml format config file
-d: using the default config, defalut config file is /foo/PhasiHunter/bin/config.yaml
-h: print help information
WARNIG: make sure choose the correct config file before run this commandSome INPUT and OUTPUT still need modified when using.
# Please provide the full path to the input file
# Configure the modules that need to be run
# y means enable, n means disable
Runing_module:
preprocess: y
phase: y
integration: y
visulization: y
initiator_prediction_and_verification:
target: y
initiator: y
deg: y
phasiRNA_target_prediction_and_verification:
phasiRNA_target: y
phasiRNA_deg: y
# Configure the preprocess module
preprocess:
# raw(mode): trim adaptor --> normalization --> length and abundance filter --> mapping
# clean(mode): normalization --> length and abundance filter --> mapping
# mapping(mode): mapping
mode: r # [r | c | m]
# for r mode: fastq file or fastq.gz file
# for c mode: fasta file or fasta.gz file
# for m mode: length and abundance filter fasta file
# ** INPUT **
inputfile: /home/user/test_osa/SRR5049781.fastq.gz
# reference sequence fasta file
# ** INPUT **
reference_fasta: # disable when index parameter enable, multiple sequence can provided here
# - /home/user/test_osa/oryza_sativa_cdna.fa
# - /home/user/test_osa/oryza_sativa_gdna.fa
# index prefix, reference_fasta option will be ignored when index enable, multiple index can provided here
# ** INPUT **
index:
- /home/user/test_osa/index/oryza_sativa_cdna_index
- /home/user/test_osa/index/oryza_sativa_gdna_index
# outfile name, relative path is work for outputfile, but absolute path is still recommended. The number must be the same as the number of reference_fasta or indexs
# ** OUTPUT **
outfile_name:
- /home/user/test_osa/SRR5049781_processed_cdna.map
- /home/user/test_osa/SRR5049781_processed_gdna.map
# adaptor trim parallel cores; <8 is recommend, only need in r mode
trim_adaptor_cores: 1
# bowtie parallel cores
bowtie_mapping_cores: 1
# max hits when mapping to ref sequence
bowtie_max_hits_cutoff: 10
# minimal sRNA reads length cutof
minimal_sRNA_length_cutoff: 19
# maxmial sRNA reads length cutoff
maxmial_sRNA_length_cutoff: 25
# sRNA reads cpm cutoff
sRNA_expression_cutoff: 1
# normalization base
library_normalization_base: 1000000
# Configure the phase module
# predicting with only one reference sequence or multiple reference sequences
phase:
# map file based on reference transcriptome sequence
# ** INPUT **
mapped_cdna_file: /home/user/test_osa/SRR5049781_processed_cdna.map
# map file based on reference genome sequence
# ** INPUT **
mapped_gdna_file: /home/user/test_osa/SRR5049781_processed_gdna.map
# map file based on full length transcriptome sequence
# ** INPUT **
mapped_flnc_file:
# reference transcritome sequence, fasta file
# ** INPUT **
cdna_fasta: /home/user/test_osa/oryza_sativa_cdna.fa
# reference genome sequence, fasta file
# ** INPUT **
gdna_fasta: /home/user/test_osa/oryza_sativa_gdna.fa
# full length transcriptome sequence, fasta file
# ** INPUT **
flnc_fasta:
# sRNA file
# ** INPUT **
sRNA_fa: /home/user/test_osa/SRR5049781_trimmed_format_filter.fa
# allsiRNA cluster output
# ** OUTPUT **
allsiRNA_cluster_output: /home/user/test_osa/phase_a.txt
# phasiRNA cluster output file
# ** OUTPUT **
phasiRNA_cluster_output: /home/user/test_osa/phase_o.txt
# phasiRNA prediction method, h(hypergeometric test) | p(phase score) | b (both)
phasiRNA_prediction_method: b
# phasiRNA cluster island
phasiRNA_cluster_island: 5
# phase length
phase_length: 21
# phase number
phase_number_cutoff: 4
# max hits when mapping to ref sequence
bowtie_max_hits_cutoff: 10
# parallel number
parallel_cores: 20
# pvalue cutoff, only function with h/b method applied
pvalue_cutoff: 0.001
# phase score cutoff, only function with p/b method applied
phase_score_cutoff: 15
# phase ratio cutoff, only function with p/b method applied
phase_ratio_cutoff: 0.4
# delete .phasiHuter_bowtieIndex, y|n
delete_index: y
# Configure the integration module
integration:
# phase module phasiRNA_cluster_output
# ** INPUT **
o_inputfile: /home/user/test_osa/phase_o.txt
# phase module allsiRNA_cluster_output
# ** INPUT **
a_inputfile: /home/user/test_osa/phase_a.txt
# reference genome gff3 file
# ** INPUT **
gff3: /home/user/test_osa/oryza_sativa_gdna.gff3
# y | n, whether exist gdna based PHAS Loci
gdna_based_PHAS_Loci: y
# integration phasiRNA cluster
# ** OUTPUT **
integration_phasiRNA_cluster: /home/user/test_osa/integration_o.txt
# integration all siRNA cluste
# ** OUTPUT **
integration_allsiRNA_cluster: /home/user/test_osa/integration_a.txt
# integration summary
# ** OUTPUT **
integration_summary: /home/user/test_osa/integration_s.txt
# PHAS Loci information
# ** OUTPUT **
integration_PHAS_Loci_info: /home/user/test_osa/integration_p.txt
# parallel number
parallel_cores: 1
# phase number
phase_number_cutoff: 4
# phase length
phase_length: 21
# pvalue cutoff
pvalue_cutoff: 0.001
# phasiRNA cluster island
phasiRNA_cluster_island: 5
# y | n, discard only P method result
discard_only_P_method_result: y
# full length transcript annotation file
flnc_annotation_file:
# Configure the visulization module
visulization:
# integration module integration_phasiRNA_cluster
# ** INPUT **
o_inputfile: /home/user/test_osa/integration_o.txt
# integration module integration_allsiRNA_cluster
# ** INPUT **
a_inputfile: /home/user/test_osa/integration_a.txt
# integration integration_PHAS_Loci_info
# ** INPUT **
p_inputfile: /home/user/test_osa/integration_p.txt
# alignment file
# ** OUTPUT **
output_alignment_file: /home/user/test_osa/alignment.txt
# phasiRNA fasta file
# ** OUTPUT **
output_phasiRNA_fa: /home/user/test_osa/phasiRNA.fa
# PHAS Gene fasta file, Format: >geneid/chr\tphasiRNA_cluster_region(start end)\tseq_region(start end)
# ** OUTPUT **
output_PHAS_fa: /home/user/test_osa/PHAS.fa
# phase length
phase_length: 21
# the number for reducing the size of Y-axis
Y_axis: 10
# reference transcritome sequence, fasta file, enable cdna based phasiRNA.fa, PHAS.fa, Alignmen, Plot output
# ** INPUT **
cdna_fasta: /home/user/test_osa/oryza_sativa_cdna.fa
# reference genome sequence, fasta file, enable gdna based phasiRNA.fa, PHAS.fa, Alignmen, Plot output
# ** INPUT **
gdna_fasta: /home/user/test_osa/oryza_sativa_gdna.fa
# full length transcriptome sequence, fasta file, enable flnc based phasiRNA.fa, PHAS.fa, Alignmen, Plot output
# ** INPUT **
flnc_fasta:
# plot cdna based phasiRNA cluster, y | n
plot_cdna_based_phasiRNA_cluster: y
# plot gdna based phasiRNA cluster, y | n
plot_gdna_based_phasiRNA_cluster: y
# plot flnc based phasiRNA cluster, y | n
plot_flnc_based_phasiRNA_cluster: n
# Configure the target module
target:
# query miRNA file, fasta format
# ** INPUT **
query_fa: /home/user/test_osa/osa.miRbase.fa
# PHAS.fa/transcript.fa, fasta file
# ** INPUT **
subject_fa: /home/user/test_osa/PHAS.fa
# output file
# ** OUTPUT **
output: /home/user/test_osa/miR_target.txt
# max. total mispairs
total_misp: off
# max. seed mispairs
seed_misp: off
# score cutoff
score: 4
# eTM search
mimics: off
# eTM stringency, (0: strict, 1: relaxed)
mimics_str: 0
# fasta36 threads
threads: 10
# Configure the initiator module
initiator:
# integration module integration_phasiRNA_cluster
# ** INPUT **
i_input_file: /home/user/test_osa/integration_o.txt
# the target predicted by psRNAtarget server or target module
# ** INPUT **
j_input_file: /home/user/test_osa/miR_target.txt
# integration module integration_PHAS_Loci_info
# ** INPUT **
p_input_file: /home/user/test_osa/integration_p.txt
# the microRNA distance away to phase border, default=105(21) or 120 (24)
sRNA_distance: 5
# 21 or 24, the phase length of 21 or 24,
phase_length: 21
# 0 or 1, the position of cleavage at 10(0) or 9-11 (1)
cleavage_shift: 1
# outputfilename
# ** OUTPUT **
outputfile: /home/user/test_osa/initiator.txt
# Configure the deg module
deg:
# mapping file for degradome data mapping transcripts, by bowtie
# ** INPUT **
inputfile:
- /home/user/test_osa/deg/GSM1040649_format_filter.map
- /home/user/test_osa/deg/GSM1040650_format_filter.map
# miRNA sequences used for target prediction, fasta
# ** INPUT **
query_fa: /home/user/test_osa/osa.miRbase.fa
# initiator module outputfile
# ** INPUT **
STI_result: /home/user/test_osa/initiator.txt
# transcripts file, fasta
# ** INPUT **
transcript_fa: /home/user/test_osa/oryza_sativa_cdna.fa
# matched map file with only matched records
# filename only, do not input directory
# ** OUTPUT **
output:
- GSM1040649_MTI_deg.txt
- GSM1040650_MTI_deg.txt
# if shifts=0 then cleaved exactly at pos.10
shift: 1
# minum number of degradome reads, int
minum_deg_abun: 0
# enable the plot function, y | n
T_plot: y
# y | n, use initiator output information
initiator: y
# 1,plot only category 1; 2, plot categories 1 and 2
plot_categories: 1
# output folder name, for exporting t-plot images and outputfile
plot_folder: MTI_deg
# library name
library:
- GSM1040649
- GSM1040650
# only output cat_1 and cat_2 information
less: y
# Configure the phasiRNA_target module
phasiRNA_target:
# query phasiRNA file, fasta format
# ** INPUT **
query_fa: /home/user/test_osa/phasiRNA.fa
# target file, fasta file
# ** INPUT **
subject_fa: /home/user/test_osa/oryza_sativa_cdna.fa
# output file
# ** OUTPUT **
output: /home/user/test_osa/phasiRNA_target.txt
# max. total mispairs
total_misp: off
# max. seed mispairs
seed_misp: off
# score cutoff
score: 4
# eTM search
mimics: off
# eTM stringency, (0: strict, 1: relaxed)
mimics_str: 0
# fasta36 threads
threads: 10
# Configure the phasiRNA_deg module
phasiRNA_deg:
# mapping file for degradome data mapping transcripts, by bowtie
# ** INPUT **
inputfile:
- /home/user/test_osa/deg/GSM1040649_format_filter.map
- /home/user/test_osa/deg/GSM1040650_format_filter.map
# phasiRNA sequences used for target prediction, fasta
# ** INPUT **
query_fa: /home/user/test_osa/phasiRNA.fa
# psRNATarget/target outputfile
# ** INPUT **
STI_result: /home/user/test_osa/phasiRNA_target.txt
# transcripts file, fasta
# ** INPUT **
transcript_fa: /home/user/test_osa/oryza_sativa_cdna.fa
# matched map file with only matched records
# filename only, do not input directory
# ** OUTPUT **
output:
- GSM1040649_PTI_deg.txt
- GSM1040650_PTI_deg.txt
# if shifts=0 then cleaved exactly at pos.10
shift: 1
# minum number of degradome reads, int
minum_deg_abun: 0
# enable the plot function, y | n
T_plot: y
# y | n, use initiator output information, for phasiRNA_deg, it must be n
initiator: n
# 1,plot only category 1; 2, plot categories 1 and 2
plot_categories: 1
# output folder name, for exporting t-plot images and outputfile
plot_folder: PTI_deg
# library name
library:
- GSM1040649
- GSM1040650
# only output cat_1 and cat_2 information
less: y# ATTENTION: The transcriptome index used for mapping degradome reads must correspond to the one utilized for predicting phasiRNAs
phasihunter preprocess -m c -i <deg_clean.fa> -mh 10 -mi 0 -ma 100 -e 1 -n 1000000 -o <deg_clean.map> -in <transcriptome index>- preprocess module
- preprocessed fasta file
- alignment file generated by bowtie
- phase module
- redundant allsiRNA cluster output
- table header: gene, strand, sRNA_position, sRNA_abundance, sRNA_record, sRNA_sequence, sRNA_length, pvalue, phase_ratio, phase_number, phase_abundance, phase_score, marker
- redundant phasiRNA cluster output
- table header: PHAS_gene, strand, phasiRNA_position, phasiRNA_abundance, phasiRNA_record, phasiRNA_sequence, phasiRNA_length, pvalue, phase_ratio, phase_number, phase_abundance, phase_score, marker
- redundant allsiRNA cluster output
- integration module
- integrated PHAS loci information
- integration summary information
- integrated allsiRNA cluster output
- table header: gene, strand, sRNA_position, sRNA_abundance, sRNA_record, sRNA_sequence, sRNA_length, phase_ratio, phase_number, phase_abundance, phase_score, pvalue, gene_annotation, marker
- integrated phasiRNA cluster output
- table header: PHAS_gene, strand, phasiRNA_position, phasiRNA_abundance, phasiRNA_record, phasiRNA_sequence, phasiRNA_length, phase_ratio, phase_number, phase_abundance, phase_score, pvalue, PHAS_gene_annotation, marker
- visulization module
- phasiRNA fasta file
- id description: recorder__PHAS_gene__position__abundance__strand__order
- PHAS loci fasta file
- id description: recorder__PHAS_gene__[start]__[end]__[extend_start]__[extend_end]__[marker]
- phasiRNA alignment result
- phasiRNA cluster plot
- phasiRNA fasta file
- initiator_prediction_and_verification
- miRNA-PHAS_loci interaction output
- Predicted phase initiator output
- vertified phase initiator output with degradome data
- degradome verification t-plot
- phasiRNA_target_prediction_and_verification
- phasiRNA-target interaction output
- vertified phasiRNA-target interaction with degradome data
- degradome verification t-plot
1.0.1 - 25/02/2024
- Ignore unplaced scaffold, mitochondrial and plastid result
- Fixed bugs that caused unexpected exit when using Ensemble or Phytozome reference.
- Fix bugs in loading files with relative paths
- Add a brief introduction about generating degradome map file
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