Question: differential expression at transcript level with paired samples
2
gravatar for mjg
4.2 years ago by
mjg20
United Kingdom
mjg20 wrote:

Dear all,

I want to do differential expression at transcript level using a rnaseq dataset that consists of paired samples (patient 1 control/treatment, patient2 control/treatment, etc.).

I have not found methods other than Ballgown and DEXSeq that are able to handle paired designs. I have also tried the option of obtaining transcript counts and use them in edgeR. However I am concerned about the fact that edgeR is not particularly adapted to do analysis on transcript counts.

Does anyone has any advice on how to go on this problem? Or if there is a way to assess my results with the latter approach I described?

Many thanks,

Maria

 

 

isoform rna-seq paired samples • 1.7k views
ADD COMMENTlink modified 4.2 years ago by Lior Pachter440 • written 4.2 years ago by mjg20
4
gravatar for Sean Davis
4.2 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

Perhaps not the solution you were looking for, but software like kallisto and Salmon (and others) generate estimates of raw counts per transcript.  You could use those estimates in edgeR or DESeq2.  

ADD COMMENTlink written 4.2 years ago by Sean Davis25k

Thanks Sean, I will consider these on my analysis.

ADD REPLYlink written 4.2 years ago by mjg20
1

If you go that route, Martin Morgan has provided code to read in kallisto output:  

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Sean Davis25k
2
gravatar for Lior Pachter
4.2 years ago by
Lior Pachter440
United States
Lior Pachter440 wrote:

The combination of kallisto-sleuth will allow you to do a transcript level analysis while taking into account your paired design.

ADD COMMENTlink written 4.2 years ago by Lior Pachter440
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