Depth of coverage

Question

[wilibaldo]

Hi all, I have a question, How do I determine the depth of coverage in a .bed file in UBUNTU?

[Ming Tommy Tang]

depth of coverage is the number of reads covered in a region. You will need the bam files and use bedtools http://bedtools.readthedocs.io/en/latest/content/tools/coverage.html

Answer 1

[wilibaldo]

thanks for the link

Answer 2

[rse]

Try using samtools for this purpose