I have files with names like:
0195_R1.fastq
0195_R2.fastq
0196_R1.fastq
0196_R2.fastq
0197_R1.fastq
0197_R2.fastq
and so on.
I need to run a software for each pair of files (the R1 and R2 are correspondent to each other) like:
bowtie2 -x index_files -1 0195_R1.fastq -2 0195_R2.fastq -S 0195_output.sam
With multiple pairs I'd have to run multiple times. So I tried to do a bash script using a for loop but I've had no success. Also, I don't know how to rename the output sequentially.
I've tried the following:
for R1 in $FQDIR/*_R1.fastq; do
for R2 in $FQDIR/*_R2.fastq; do
bowtie2 -x index_files -1 $R1 -2 $R2 -S $N_output.sam
done
done
What should I do?
If you loop over all the R1 and R2 files, you'll run bowtie
for all possible pairs of data files. If I understand correctly, that's not what you want - you only want to process the corresponding pairs.
To do that, loop over R1 files only, and try to find the corresponding R2 file for each:
#!/bin/bash
fqdir=...
for r1 in "$fqdir"/*_R1.fastq; do
r2=${r1%_R1.fastq}_R2.fastq
if [[ -f $r2 ]] ; then
bowtie2 -x index_files -1 "$r1" -2 "$r2" -S "$N"_output.sam
else
echo "$r2 not found" >&2
fi
done
I'm not sure what $N
stands for. Maybe you can use $r1
instead?
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