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Revision d1ea2969986b335ff6e0d00b4b95332ac052c430 authored by Hervé Seitz on 09 June 2020, 14:40:32 UTC, committed by GitHub on 09 June 2020, 14:40:32 UTC 
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Script_align.sh 
#!/bin/sh
if test "$1" = ""
then echo "Sample list?"
     read list
else list=$1
fi

for sample in `cat $list`
do hisat2 -x ~/Genomes/Mus_musculus/UCSC/mm10/Sequence/HISAT2Index/genome -1 $sample'_R1.fastq' -2 $sample'_R2.fastq' -S Mapping_default_parameters_$sample'.sam'
done
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