[BioC] suggestions/comments on DESeq transcript wise analysis

[Abhishek Pratap]

Unless you are counting reads on the unique disjoin set of exons from
the transcripts , double counting will be inevitable as most of the
transcripts for a gene will have overlapping  exons.

You can also see Simon's post today on a different thread about the
same issue. He explains in more detail why one would want to stay with
gene level or exon level differential expression and relate it back to
gene/isoforms.

-Abhi

On Thu, Feb 9, 2012 at 9:06 AM, Akula, Nirmala (NIH/NIMH) [C]
<akulan at mail.nih.gov> wrote:
> Based on the previous threads when using DESeq the reads should not be double counted. I am following pipeline for RNA-seq analysis and would like to know any suggestions/comments regarding the pipeline:
>
>
>  1.  Mapping the reads using Tophat
>  2.  Convert Tophat output.bam to Sam
>  3.  Create bed file from Sam file
>  4.  Use CoverageBed along with reference genome for counting the reads
>  5.  Sum count of reads from all exons in a transcript
>  6.  DESeq to analyze the counts/transcript
>
> Thank you very much
> Nirmala
>
>
>
>
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