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HISAT2 paired end multiple files loop error

Hi, I got stuck with running hisat2 with a loop.

my input files are here,

enter image description here

here is my loop code,

for f in `ls -1 *_1_fp.fastq.gz | sed 's/_1_fp.fastq.gz//' `
do
hisat2 -rna-strandness RF -x GRCm39 -1 ${f}_1_fp.fastq.gz -2 ${f}_2_rp.fastq.gz 2> ${f}.log| samtools view -@ 8 -Sbo ${f}.bam
done

the error message is,

enter image description here

help me, please.

hisat2 rna-seq
• 1,394 views • link
updated by GenoMax GenoMax • written by SH • SH

The back-tick is in the wrong place.

First line should be

for f in `ls -1 *_1_fp.fastq.gz` | sed 's/_1_fp.fastq.gz//'

Always add an echo command to your loops to make sure the output looks reasonable before removing it to actually execute the commands.

• 0 views • link
written by GenoMax GenoMax

I'd tried several times, but,

enter image description here

• 0 views • link
written by SH • SH

Are you using a mac? If so, make sure you are typing the - symbols by hand. If you are copying pasting this command from someplace then those may be getting turned into smart hyphens.

• 0 views • link
written by GenoMax GenoMax

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