How to let `trim_galore ` resolve multiple Regex file names?

How to let `trim_galore ` resolve multiple Regex file names?

0

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!


trim_galore

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2 hours ago by


Dan

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