Question: How To Use R To Segment Genome And Count Reads From Sequencing Data?
gravatar for C Shao
6.6 years ago by
C Shao130
C Shao130 wrote:

Hi everyone:

I have some whole-genome sequencing data, now I would like to segment human genome (1:22, X,Y) to nonoverlap equal size bins and count reads within it, defining by the location of fire base of one read.

What to do this only through R?

I am trying Rsamtools but didn't get any solution. Could some help me on this?


ADD COMMENTlink written 6.6 years ago by C Shao130
gravatar for Michael Dondrup
6.6 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

In addition to Rsamtools to read your bam file you will need the IRanges package, have a look at the countOverlaps function, and the function successiveIRanges to generate interval bins. If you are experiencing problems, please post a code example to improve.

ADD COMMENTlink written 6.6 years ago by Michael Dondrup46k
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