next-gen sequencing analysis
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7.0 years ago
onemore100iq ▴ 20

how to generate depth for all positions on chromosome_3 for specific strain bam.file and relate it to the full length of chromosome_3 in its reference genome which has length of 10039875.

next-gen • 1.3k views
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this is what i wrote and did not work:

samtools depth -a chromosome_3:0-10089875 starin bamfile.bam

it gave me error message " could not open "chromosome_3:0-10089875" no such file or directory"

any help please.

Thanks

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