Param.in

# Start: 2
# Stop:  9
#
# \\  1 - Download the data
# \\  2 - Perform adapter trimming on downloaded FASTQ files
# \\  3 - Perform quality filtering on trimmed FASTQ files
# \\  4 - Remove sequences that align to non-coding RNAs from the filtered FASTQ files
# \\  5 - Align sequences to the genome from the ncRNA subtracted FASTQ files
# \\  6 - Create Raw Assignment from the genome aligned sorted/indexed BAM file
# \\  7 - Create Metagene tables
# \\  8 - Create Metagene plots
# \\  9 - Corrected assignment
#
# Clean: rm
#
# \\ gzip  - Gzip files after they are no longer necessary
# \\ rm    - Remove files after they are no longer necessary
#
# Quality: 0.80
#
# \\ Quality filter threshold for retaining reads (0.0 - 1.0). Higher is more selective.
#
# Mapping: 5
#
# \\ 5 - Map reads according to their 5' end
# \\ 3 - Map reads according to their 3' end
#
# ReadLenMiN: 19
# ReadLenMaX: 32
#
# \\ 25 - ReadLenMiN length of reads included -! going to replace Length
# \\ 35 - ReadLenMaX length of reads included -! going to replace Length
#
# Normalised: rpm
#
# \\ rpm - use normalized data - reads per miljon
# \\ raw - raw counts
#
# MappedTwice: No
#
#  \\ No or Yes IF Yes include reads mapped once and twice
#
# Save2csv: False
#
#  \\ boolean - False or True
#
# MetagThreshold: 20
#
# \\ 30 - raw counts around start or stop if less ignore a gene/region
# \\ If Normalized = "rpm"  MetagThreshold is readjusted by dividing normalization_factor inside program
# \\ FILTER 3
#
# MetagSpan: 60
#
# \\ 60 - number of nucleotides before and after start/stop in metagene profiles
#
# MetagSpancorr: 120
#
# \\ 90 - number of nucleotides before and after start/stop in metagenomic profile from corrected data
#
#
# OffsetFile: readlength_offsets.txt
#
# \\ file with read length and offsets - only these readlength are included into corrected/final assignment
#
# cpu: 6
#
# \\ number of cores - have effect in some steps
#

ERR3218438	S1_WT_30C_rep1
ERR3218439	S3_WT_30C_rep2
ERR3218430	S2_KO_30C_rep1
ERR3218431	S4_KO_30C_rep2
ERR3218434	S5_WT_20C_rep1
ERR3218435	S7_WT_20C_rep2
ERR3218426	S6_KO_20C_rep1
ERR3218427	S8_KO_20C_rep2