[BioC] summarizeOverlaps using GRanges or bed file as reads?

Ryan C. Thompson rct at thompsonclan.org
Tue Apr 15 03:08:36 CEST 2014


I would like to manipulate the start and end positions of my reads 
before calling summarizeOverlaps. One way to do this is to convert my 
reads to a GRanges and then use flank, narrow, etc. to properly position 
the read ends where I want them. However, I don't see a method for 
summarizeOverlaps that accepts a GRanges object or bed file or similar 
for the reads. Is there such a method, and if not, would it be possible 
to add it?

The specific application I have in mind is single-end ChIP-Seq reads, 
where we have a good idea of what the fragment length is and would like 
to extend the reads to this length. Alternately, it may be preferable to 
count only the 5-prime ends of the read, and this could be done by 
narrowing to 1 bp length.

-Ryan Thompson

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