next-gen sequencing analysis

Question

[onemore100iq]

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.

[onemore100iq]

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

Answer 1

[Nicolas Rosewick]

check bedtools genomecov : http://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html