Entering edit mode
7.7 years ago
simo017
▴
10
I have the following sed command that change the chromosome name:
for file in /myoldpath/*.bam
do
filename=echo $file | cut -d "." -f 1
samtools view -H $file | sed -e 's/SN:([0-9XY])/SN:chr\1/' -e 's/SN:MT/SN:chrM/' | samtools reheader - $file > /mynewpath/${filename}_chr.bam
done
My quesion is how to insert the result in a new path while keeping the variable $filename
as part of every new file name? it always insert the result in /myoldpath/
or literally "filename.chr.bam
" in the /mynewpath/
am i missing something in the syntax of that part "$file > /mynewpath/${filename}_chr.bam
"?
thank you in advance
Thank you @Goutham
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