Question: Cuffmerge files contain different number of lines depending on reference annotation file - why is that?
gravatar for marvin.holz
3 months ago by
marvin.holz0 wrote:

Hey guys,

maybe I got the purpose of using cuffmerge wrong, but I thought it creates a file including all transcripts that are present in a certain number of samples (e.g. my whole experiment).

I get an output of 97,000 lines running cuffmerge without an annotation file. Using two different .gtf files (NCBI refSeq or UCSC refgene) I get 2.4 million lines or 970,000. How is that possible? And which is the correct one?


cuffmerge annotation output • 116 views
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