[BioC] summarizeOverlaps mode ignoring inter feature overlaps

[Wei Shi]

Dear Tom,

Please see my reply below.

On Apr 11, 2013, at 12:55 PM, Thomas Girke wrote:

> Dear Wei,
> 
> Thanks. I guess this makes sense, but is it possible this way to perform
> transcript level counting in addition to exonic gene-level counting? 
> 

Yes, it can do that. But you will have to provide your own transcript annotation. Rsubread only includes RefSeq annotation for exons.

> Also, this reminds me of one question related to Rsubread for which I
> couldn't find an answer in the documentation (haven't had time to read
> your NAR paper though). Is it possible to use Rsubread for aligning
> directly against transcriptome sequences where we want to set no
> restrictions on multiple mappings of equal quality in order to obtain
> transcript read counts? Right I am often doing this with Bowtie2 for our
> own transcriptome assemblies where we don't have a reference genome and
> then use Rsamtools for counting the reads mapping to individual
> transcripts. With Rsubread I was not sure if the algorithm can return
> any number of alternative hits? If it can then I would love to give it 
> a try for our transcriptome assembly projects.
> 
> Thomas
> 
> 

Rsubread reports no more than one mapping location for each read. But we probably should provide an option to allow multiple mapping locations to be reported for the reads. This should be pretty straightforward to do. I will let you know once we added this option (probably in a couple of days).

Cheers,
Wei






______________________________________________________________________
The information in this email is confidential and intend...{{dropped:6}}