RNA-seq analysis

[jy123]

I am doing RNA seq analysis for different gene expression analysis. I find that people use two approaches:

1. Tophat - HtSeq - edgeR or DESeq R package
2. Tophat - Cufflinks -Cuff Diff

which approach that your guys use most? any advice?

[pbseq]

I am in an early phase of my RNA-seq project and by now I'm using DESeq and edgeR for estimating modulated genes (DEG) and cufflinks /cuffcompare/cuffdiff for exploring differentially expressed transcripts, differential splicing and differential promoter use.

if I also use cufflinks for estimating DEGs, I usually get some 50% DEGs in common with DESeq. DESeq and edgeR, on the other hand, share 80% of estimated DEGs.
I am still experiencing things but I guess that the % of common DEG between DESEq and cufflinks is very much influenced by how you run cufflinks (reference GTF or not and other parameters as -R when running cuffcompare).
I didn't try the latest cufflinks version yet, however. I used version 0.9.3

It would be nice getting inputs on what others are doing !
hope it helps,

pbseq

[lpachter]

Just wanted to let you know that Cufflinks 1.0 has a completely revamped approach to DE that models over-dispersion of counts at the transcript level and we'll be curious to know how it performs on your tests.

[pbseq]

lpatcher,
for sure I'll try soon latest version of cufflinks !

[Navi]

Hello,

I want to analyze my RNASeq data using DESeq. Would anyone tell me how and where to find codes for DESeq? Thx

[Simon Anders]

What do you mean by "codes"?

We have written a nice manual (a "vignette") for DESeq, which you find here. We are currently overhauling it, and you'll find the improved vignette soon here.

[Navi]

Thank you Simon.

[Navi]

Hi Simon, how can I get TagSeqExample.tab file for practice?

[Navi]

I got it