Counting read ends in RNA-Seq
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7.2 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 • 1.3k views
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7.2 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

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7.2 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

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7.2 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.

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