gravatar for amitpande74

3 hours ago by

I have BAM files in the external hard drive. Want to convert them into BED. Am using

cd /media/usr/LaCie/work/client/pool1/bam
for x in *.bam ; do
    echo "print current:$x";
    bedtools bamToBed -i "$x" > "${x%.bam}.bed";
done
echo "done"

it writes the BED files in the directory, but they are all empty. My BEDtools is installed in

/home/usr/miniconda3/bin/bedtools

Can someone tell me where I am going wrong? And the BAM files have reads, so there is no problem there.
regards.



Source link