Question: featurecounts flags for lncRNA and mRNA co-expression
gravatar for Sam
4 months ago by
Sam110 wrote:

Dear Biostars

I predicted some lncRNAs transcript according to RNA-seq data and then I used featurecounts to count the lncRNAs transcript (-t exon and -g transcript_id ) in the BAM files. for lncRNA/mRNA co-expression analysis, should I count mRNAs according to transcipt_id or gene_id (-t exon and -g gene_id)?


ADD COMMENTlink modified 4 months ago • written 4 months ago by Sam110
gravatar for JC
4 months ago by
JC8.0k wrote:

My suggestion is you need to test both, at the gene level, isoforms can be expressed differently between treatments, or not.

ADD COMMENTlink written 4 months ago by JC8.0k

featurecounts with -g transcript_id give about 20% less DE mRNAs compare to grouping according gene_id. so is it expected to have less DE in transcript level? I think if we compare transcript vs. transcript( for mRNAs vs. lncRNAs transcript correlation), it could produce more robust data. is it true?

ADD REPLYlink written 4 months ago by Sam110

Robust it not fair comparing genes (which are the sum of all isoforms) and just transcripts. Some genes can be no differential but some isoforms could be. That also doesn't give a good idea if the change is biologically important. I am more on the side to do both analyses and check if the results make sense biologically.

ADD REPLYlink written 4 months ago by JC8.0k
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