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

[Wei Shi]

Dear Ryan,

I'm not entirely sure what you are trying to do. But would extending the genomic regions you use in your summarization achieve the same effect?

For your second request, maybe you can do a filtering after you get the read counts, which is pretty straightforward to do?

Best wishes,

Wei

On Apr 8, 2014, at 11:19 AM, Ryan C. Thompson wrote:

> Hello,
> 
> 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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