Hi everyone,
I aligned my reads using tophat and loaded the results in R to do the DE analysis using DESeq. I feed it an exon annotation and get DE exons. So far so good. I would now like to identify DE mRNAs from these DE exons. I can think of several ways of doing this but would like to know if anyone else has done this before and how it is "usually" done...
For example: identify the transcripts for which "most" (threshold) of the present exons (count > threshold2) have a FC > 2 (significant) and call them as DE...
Or maybe I am missing something...
Thanks a lot!
I aligned my reads using tophat and loaded the results in R to do the DE analysis using DESeq. I feed it an exon annotation and get DE exons. So far so good. I would now like to identify DE mRNAs from these DE exons. I can think of several ways of doing this but would like to know if anyone else has done this before and how it is "usually" done...
For example: identify the transcripts for which "most" (threshold) of the present exons (count > threshold2) have a FC > 2 (significant) and call them as DE...
Or maybe I am missing something...
Thanks a lot!
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