Problems with alignment in bash mode with hisat2

Question

[Peter]

I'm trying to align paired-end sequences with the following loop:

for f in `ls *.fq.gz | sed 's/_0[12].fq.gz//g' | sort -u`

 do

hisat2 -p 8 -x /home/referenceData/GRCh37_index -1 ${f}_1 -2 ${f}_2 -S ${f}.sam | samtools view -@ 8 ${f}.sam > ${f}.bam | samtools sort -@ 8 ${f}.bam -o ${f}.sorted.bam
done

However, this command is not running, because I am getting this error:

"SRR10042682_1_val_1.fq.gz_1: No such file in the directory"

"SRR10042682_2_val_2.fq.gz_2: No such file in the directory"

My samples are named as follows: SRR10042682_1_val_1.fq.gz and SRR10042682_2_val_2

can anybody help me?

Thanks!

[cpad0112]

You are not reconstituting input files. Try this and echo before you run the command:

for f in `ls *.fq.gz | sed 's/_[12]_val_[12].fq.gz//g' | sort -u`

I would prefer this way, in a shell in the absence of parallel:

$ for f in *_1.fq.gz ; do echo $f ${f%%_*}_2_val_2.fq.gz; echo ${f%%_*}.{b,s}am;done

SRR10042682_1_val_1.fq.gz SRR10042682_2_val_2.fq.gz
SRR10042682.bam SRR10042682.sam

[ATpoint]

What's the zero in the sed command supposed to do in your opinion?