Closed:Count the number of reads for multiple genomic locations on different (not all) chromosomes
3
0
Entering edit mode
6.0 years ago
vkgaur25 ▴ 30

I have a Illumina cancer panel data and after generating a bam file I want to find the total number of reads mapped to genome on some coordinates that I got from a bed file. I know that I can do that using samtools view while mentioning the exact position but I have 212 coordinates to look at and if I give a bed file mentioning 212 coordinates with bam file it would output a file containing reads and other details with coordinates but not total counts of reads in every single coordinate. How can I do that?

RNA-Seq • 582 views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 1790 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6