Alternative to CuffDiff

[sphil]

Hey there,

i am going to do some DE stuff with tophat-cufflinks-cuffdiff pipeline. But, is there any other tool like cuffdiff which can compute isoform abundances? I just want to get a 2nd opinion.
I know there are some for R but since it is a human RNA-seq exp. i doubt R can handle it.

best,


Philip

[cjp]

Scripture?

http://www.broadinstitute.org/software/scripture/

Chris

[steven]

Flux Capacitor?
http://flux.sammeth.net/
(not sure about DE test though)

[sphil]

thanks for your reply. I mainly need an equivalent to cuffdiff...

[kopi-o]

Your question is a bit unclear, as Cuffdiff does not "compute isoform abundances" (Cufflinks does that.)

Alternatives to Cuffdiff (for assessing differential expression) would be e.g. DESeq och edgeR, the R packages you probably had in mind. They will easily handle human data as the input is just a table of read counts per gene or transcript.

If you want to detect differential expression between isoforms (rather than genes), you could look at DEXSeq.

If you are in fact looking for a way to quantify isoform abundances, you could check out RSEM, MISO, rpkmforgenes.py, just to mention a few.

[sphil]

hey,

sry if it is / was unclear.

I will try DEXSeq cause i want to detect DE between isoforms if possible!


Thanks a lot!


best,

Philip