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13 months ago
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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.
The back-tick is in the wrong place.
First line should be
Always add an
echo
command to your loops to make sure the output looks reasonable before removing it to actually execute the commands.I'd tried several times, but,
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 intosmart hyphens
.