Hi Steve,

Thank you for your reply,

I just want to known what is the idea feature for summarizing read count
after alignment?. Gene,transcript,exons features from GFF/GTF files are
frequently used .

Thanks


On Thu, Oct 31, 2013 at 11:43 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi Reema,
>
>
> On Thu, Oct 31, 2013 at 10:04 AM, Reema Singh <reema28sep@gmail.com>
> wrote:
> > Dear All,
> >
> > I would like to known in order to find out the differentially expressed
> > genes between two condition - what is the idea feature for
> summarization? .
> > I have choosen gene by summarization. Is this a good choice?.
> >
> > Any suggestions would be very helpful.
>
> You're going to have to ask a more specific question, as I'm having a
> hard time understanding what you are after.
>
> If you are just curious how you could perform a differential
> expression analysis, there are workflows you can read through here:
>
> http://bioconductor.org/help/workflows/
>
> Different packages that perform these analyses are also very well
> documented, including:
>
> * The limma user's guide: this can be applied to both microarray and
> rna-seq analysis
> * edgeR user's guide: differential rna-seq expression
> * DESeq2 vignette: differential rna-seq expression
> * DEXSeq vignette: differential exon usage using rna-seq data
> * oligo: different types of array analyses (including expression,
> tiling, and exon arrays)
> * xps: similar types of analyses to oligo (I think).
>
> Enjoy,
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>



-- 
Reema Singh
PhD Scholar
Computational Biology and Bioinformatics
School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi-110067
INDIA

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