Question: Differential expression in edgeR with cuffdiff count output
gravatar for mjg
4.6 years ago by
United Kingdom
mjg20 wrote:


I have rna-seq data from paired samples and want to do isoform-level differential expression. 

My understanding is that is not possible to explicitly specify paired design in cuffdiff, so I considered the option of using the isoforms.read_group_tracking file and extract the 'raw_frags' column, which I *think* corresponds to counts. Then use this as input in edgeR where I can specify paired-sample design.

Does this sound sensible?

If not, my question is: which package can I use to do isoform-level DE which takes into consideration paired-sample designs.





edger rna-seq cuffdiff • 1.9k views
ADD COMMENTlink modified 4.5 years ago by Lior Pachter480 • written 4.6 years ago by mjg20
gravatar for mark.ziemann
4.6 years ago by
mark.ziemann1.2k wrote:

DEX-Seq Estimates exon usage coefficients from the fitted terms of the GLM and may be just what you're looking for.

ADD COMMENTlink written 4.6 years ago by mark.ziemann1.2k

Thank you for your suggestion! I did not know about DEX-Seq, I am running it now and will compare it with my previous results. 


ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by mjg20
gravatar for Lior Pachter
4.5 years ago by
Lior Pachter480
United States
Lior Pachter480 wrote:

You can use sleuth.

ADD COMMENTlink written 4.5 years ago by Lior Pachter480

I have played sleuth. But if I am interested with DE genes but not DE transcripts in downstream analysis, how could I do it with sleuth?

e.g. I got the DE transcripts table with Q<0.05 with associated gene name. But as you know, one gene could have multiple transcripts.


target_id          Q                        ext_gene
ENST00000257570    0                        OASL
ENST00000339275    1.08823325997074e-138    OASL
ENST00000543677    4.50865532164411e-20     OASL

Could I use it for finding DE genes like edgeR/DESeq? how?

Thank you!

ADD REPLYlink modified 7 weeks ago by RamRS25k • written 4.1 years ago by super60
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