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Old 01-17-2013, 07:22 AM   #1
Junior Member
Location: hangzhou

Join Date: Dec 2012
Posts: 3
Default how to do test on RNA-seq data like this

Hi, all

I have two groups of RNA-seq data (A and B), with both two biological replicates within groups(A1, A2 and B1, B2). For each replicate, the reads are mapped two genomes(X,Y). Now i have counted the mapped reads for each orthologs between X and Y. Next, i want to do statistic test on expression ratio of X/Y between groups. I don't know which model or method could be used, anyone who can give suggestions. Thanks.
shuixiangyuer is offline   Reply With Quote
Old 01-17-2013, 09:27 AM   #2
Location: Freiburg

Join Date: Oct 2012
Posts: 56

I am in a similar position and what I have chosen to do, is to run the Tophat - Cufflinks - Cuffdiff - cummeRbund pipeline. In addition, I am running Tophat - HTseq - DESeq.

In the end, my idea is to end up with two lists of DE genes and then intersect them. Those genes captured by both techniques must for sure be DE.
DonDolowy is offline   Reply With Quote

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