HISAT2 paired end multiple files loop error

Question

[SH]

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

my input files are 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,

help me, please.

[GenoMax]

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.

[SH]

I'd tried several times, but,

[GenoMax]

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.