Bash Script Loop Help

Question

[V]

Hello,

I'm trying to run hisat on loop and I've been trying to modify an existing loop I had set up but can't get it to work with my new file names.

My R1 is called WTCH_1_val_1.fastq and my R2 is called WTCH_2_val_2.fastq, where every time WTCH is actually a different value to distinguish the difference samples. This is the loop I was using so far when all of my samples were WTCH_1.fastq and WTCH_2.fastq

for f in `ls -1 *_1.fastq.gz | sed 's/_1.fastq.gz//' `
do
echo hisat2 -x mm10idx -1 ${f}_1.fastq.gz -2 ${f}_2.fastq.gz -S ${f}.bam
done

Could someone that is much better at this than I am please modify it for me? thanks

[h.mon]

Just replace every instance of .fastq.gz with .fastq and it should work.

[V]

I've tried that but it doesnt work sadly, the echo returns:

hisat2 -x mm10idx -1 WTCHG_465974_296190_1_val_1.fq.gz -2 WTCHG_465974_296190_1_val_2.fq.gz -S WTCHG_465974_296190_1_val.bam

The loop as is thinks that the R2 finishes in "_1_val_2.fq.gz" but it finishes in "_2_val_2.fq.gz" the issue is the first _2 I think.

Answer 1

[h.mon]

Revise and clean up your post: you are using .fastq, .fastq.gz and .fq.gz, with no indication on which is the correct.

If your files are named ${whatever}_1_val_1.fastq.gz and ${whatever}_2_val_2.fastq.gz, then:

for f in `ls -1 *_1.fastq.gz | sed 's/_1_val_1.fastq.gz//' `
do
echo hisat2 -x mm10idx -1 ${f}_1_val_1.fastq.gz -2 ${f}_2_val_2.fastq.gz -S ${f}.bam
done

[V]

Sorry for the confusion, had mixed version of it. All sorted now with your post. Thanks alot! works like a charm.