[BioC] easyRNAseq question
Simon Anders
anders at embl.de
Thu May 31 08:30:44 CEST 2012
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
More information about the Bioconductor
mailing list