How to let `trim_galore ` resolve multiple Regex file names?
Hello
In ATACseq and ChIP-seq, I have multiple *R1_001.fastq.gz
and multiple *R2_001.fastq.gz
files for each sample. When I supply Regex file names to trim_galore
using bash script trim_galore.bash
:
# 3 arguments of the script: 1. directory of FASTQ, 2. R1 fastq 3. R2 fastq
trim_galore --cores 4 --illumina --paired --fastqc -o trim_galore $1/$2 $1/$3
and
trim_galore.bash fastq/sample1 sample1*R1_001.fastq.gz sample1*R2_001.fastq.gz
trim_galore.bash fastq/sample2 sample2*R1_001.fastq.gz sample2*R2_001.fastq.gz
trim_galore
only treats the first 2 R1_001.fastq.gz
files.
I have to merge all the R1
and R2
files first, before running trim_galore
.
Is it possible for trim_galore
to trims all the multiple R1/R2
files for each sample without merging them?
Thank a lot!
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