Making comparison of lowly expressed transcripts

hugomarquez · 10-27-2013, 08:37 PM

I have been give a project where I need to compare the expression pattern of a lot of lowly expressed transcripts. As I know, Cufflinks discard those transcripts directly thus can't be used. Does anyone have any suggestions? Thanks!

dpryan · 10-28-2013, 02:24 AM

You could just use one of the count-based methods (edgeR/DESeq/etc.) and just not do any filtering.

hugomarquez · 10-31-2013, 04:24 PM

Thanks so much!

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10-27-2013, 08:37 PM	#1
hugomarquez Member Location: earth! Join Date: Oct 2013 Posts: 15	Making comparison of lowly expressed transcripts I have been give a project where I need to compare the expression pattern of a lot of lowly expressed transcripts. As I know, Cufflinks discard those transcripts directly thus can't be used. Does anyone have any suggestions? Thanks!

10-28-2013, 02:24 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	You could just use one of the count-based methods (edgeR/DESeq/etc.) and just not do any filtering.

10-31-2013, 04:24 PM	#3
hugomarquez Member Location: earth! Join Date: Oct 2013 Posts: 15	Thanks so much!