[BioC] easyRNAseq question

[Simon Anders]

Dear Nirmala

On 2012-05-27 02:25, Akula, Nirmala (NIH/NIMH) [C] wrote:
> I used HTSeq (similar to your geneModel method) which takes the
> counts of disjoint exons for the genes. The problem with this method
> is that too many reads are assigned to ambiguous category and
> sometimes total number of reads that fall on disjoint exons are too
> few to get a valid DESeq result. Using RefSeq genes the total number
> of genes counted by HTSeq on my data is ~14000 whereas using the
> bestExon method we get ~22000. Do you observe similar counts with
> your data?

It does not quite make sense that counting only for the best exons gives 
you more counts than counting for all exons.

Could it be that the issue with UCSC GTF files described here is the 
source of your problems:

https://stat.ethz.ch/pipermail/bioconductor/2012-April/044717.html

   Simon