[BioC] Feature request for Rsubread::featureCounts: read length adjustment

Ryan C. Thompson rct at thompsonclan.org
Tue Apr 8 03:19:35 CEST 2014


I would like to request a simple feature for Rsubread's featureCounts 
function that would make it more useful for ChIP-Seq applications. I 
want to use featureCounts to count the number of reads falling in each 
of my called peaks. However, each read represents a DNA fragment of a 
specific length, which can be estimated by cross-strand correlation 
analysis or known a priori. In my case, it is the length of one 
nucleosome, i.e. 147 bp. So I would like to treat each read as being 147 
bp long for the purpose of computing overlaps, since the number of bp 
sequenced is not representative of the fragment length. Would it be 
possible to add a parameter to featureCounts to allow this adjustment? 
Also, an additional feature that would be nice to have, but is less 
important, would be the ability to require that a certain percentage of 
a read overlaps a feature before counting it.

Thanks for listening,

-Ryan Thompson

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