Counting read ends in RNA-Seq
3
0
Entering edit mode
6.8 years ago
cmacprobst • 0

How to count (depth) of the read last (or first) base per position and not reads per position?

I need to identify the mRNA boundaries to see events of splicing.

RNA-Seq • 1.2k views
ADD COMMENT
0
Entering edit mode
6.8 years ago
tarek.mohamed ▴ 370

Hi,

If you have your sam/bam files, you can calculate the depth using samtools.

http://www.htslib.org/doc/samtools.html

Tarek

ADD COMMENT
0
Entering edit mode
6.8 years ago
cmacprobst • 0

But depth commonly means: N of reads that map in a X position.

I need N of read match end (or N of read match start) in a X position.

Dealing with CIGAR is a little troublesome, so I am asking if there is a tool or option that can do this.

TIA Christian

ADD COMMENT
0
Entering edit mode
6.8 years ago
Asaf 10k

I once wrote a script to do that. See: https://github.com/asafpr/RNAseq_scripts/blob/master/sam_to_wiggle_coverage.py

You can run it with -f flag to count only the first position of the read, -r should read the first position of the second read or the end of the read. Please go over the script since I haven't used it for quite a while and it comes without responsibility.

ADD COMMENT

Login before adding your answer.

Traffic: 2885 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