[BioC] girafe issues - no interval overlap

[Hervé Pagès]

On 03/31/2011 03:50 PM, karlerhard at berkeley.edu wrote:
> Hi list,
>
> I've identified what I think is a problem in my girafe analysis: I am
> getting ZERO overlaps between my aligned read intervals (from BAM file)
> and my annotation intervals from the interval_overlap function used in the
> girafe package.
>
> I'm pretty sure that the BAM file is ok, it inputs fine and is recognized
> as an "AlignedGenomeIntervals" object using class(my_bamfile). Although
> I'm using a subset of my dataset for troubleshooting, I've checked (with
> my own eyes) and there are definitely intervals in this list that do
> overlap with intervals from my gff file.
>
> So I suspect there is some formatting issue with my gff file, but I'm not
> sure what it is.
>
> I'll keep searching, but if anyone has an idea as to what could be causing
> this discrepancy, it would be super.

You might want to provide a small, self contained, reproducible example
to make it easier for others to look at this problem. Thanks!

H.

>
> karl
>
> Grad Student - UC Berkeley
>
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-- 
Hervé Pagès

Program in Computational Biology
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