Not directly relevant to gene-level RNA-seq DE calls, but rather for
exon-level DE,
I found it useful to read this:
http://precedings.nature.com/documents/6837/version/1
In particular, section 4.3 on page 11, and supplementary figures S7 and S8
on page 19.

I was informed by a coworker that since everyone uses
BowTie-TopHat-Cufflinks-Cuffdiff, it is the sensible thing to do.
Conversations with people who know what they are doing (Terry Speed &
BCGSC) suggest the matter is not yet settled.
So I retrieved ~1TB of BAMs, extracted the reads, and started looking into
how that compares to DEXSeq and/or subread.

It would be incredibly informative if the Cufflinks and DEXSeq authors had
time to weigh in on their strengths/weaknesses. DEXSeq & cummeRbund both
offer nice tools for exploring the results; I am curious which pipeline
fits best for my needs.

Thanks for bringing this up.


On Mon, Feb 13, 2012 at 8:01 AM, Richard Friedman <
friedman@cancercenter.columbia.edu> wrote:

> Dear Bioconductor list,
>
>        Sometime ago Simon Anders explained the difference
> between DeSeq and Cuffdiff as follows:
>
> "If you have two samples, cuffdiff tests, for each transcript, whether
> there is evidence that the concentration of this transcript is not the
> same in the two samples.
>
> If you have two different experimental conditions, with replicates for
> each condition, DESeq tests, whether, for a given gene, the change in
> expression strength between the two conditions is large as compared to
> the variation within each replicate group."
>
> Current language on the Cuffdiff site suggests that the current version
> of that program  tests for whether the change is significant compared to
> changes in each condition.
>
> http://cufflinks.cbcb.umd.edu/**howitworks.html#hdif<http://cufflinks.cbcb.umd.edu/howitworks.html#hdif>
>
> http://cufflinks.cbcb.umd.edu/**howitworks.html#reps<http://cufflinks.cbcb.umd.edu/howitworks.html#reps>
>
> Can someone please comment on the relative merits of Cuffdiff and
> DeSeq. I ask here because our sequencing core delivers results
> based on Cuffdiff and I want to know if I should redo it using
> DeSeq,I would greatly appreciate any guidance in this matter.
>
> Thanks and best wishes,
> Rich
> ------------------------------**------------------------------
> Richard A. Friedman, PhD
> Associate Research Scientist,
> Biomedical Informatics Shared Resource
> Herbert Irving Comprehensive Cancer Center (HICCC)
> Lecturer,
> Department of Biomedical Informatics (DBMI)
> Educational Coordinator,
> Center for Computational Biology and Bioinformatics (C2B2)/
> National Center for Multiscale Analysis of Genomic Networks (MAGNet)
> Room 824
> Irving Cancer Research Center
> Columbia University
> 1130 St. Nicholas Ave
> New York, NY 10032
> (212)851-4765 (voice)
> friedman@cancercenter.**columbia.edu <friedman@cancercenter.columbia.edu>
> http://cancercenter.columbia.**edu/~friedman/<http://cancercenter.columbia.edu/~friedman/>
>
> I am a Bayesian. When I see a multiple-choice question on a test and I
> don't
> know the answer I say "eeney-meaney-miney-moe".
>
> Rose Friedman, Age 14
>
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>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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