Question: Differential expression in edgeR with cuffdiff count output
0
gravatar for mjg
3.7 years ago by
mjg20
United Kingdom
mjg20 wrote:

Hello,

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.

 

Thanks,

Maria

 

edger rna-seq cuffdiff • 1.7k views
ADD COMMENTlink modified 3.7 years ago by lakigigar220 • written 3.7 years ago by mjg20
1
gravatar for mark.ziemann
3.7 years ago by
mark.ziemann1.1k
Australia/Mebourne/Geelong/Deakin
mark.ziemann1.1k wrote:

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

http://www.bioconductor.org/packages/release/bioc/manuals/DEXSeq/man/DEXSeq.pdf

ADD COMMENTlink written 3.7 years ago by mark.ziemann1.1k

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. 

Maria
 

ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by mjg20
1
gravatar for lakigigar
3.7 years ago by
lakigigar220
United States
lakigigar220 wrote:

You can use sleuth.

ADD COMMENTlink written 3.7 years ago by lakigigar220

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.

like

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 3.2 years ago • written 3.2 years ago by super60
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