Cuffcompare: Some Cufflinks Transcripts Are Not Contained By Cuffcompare Output Tmap File

Question

[zju.whw]

I'm using the tophat/cufflinks/cuffcompare tools to deal with the RNAseq to assemble the transcriptome. When I use cuffcompare to compare Cufflinks transcript gtf file with the annotation gtf file, the output tmap lost some transcript id in my Cufflinks transcript gtf file. As the Cufflinks' manual saying, "there is one row per Cufflinks transcript". However, the cufflinks transcript has 44499 unique id and the tmap has 44246 lines. Most of the lost id has 0 fpkm, but there are also 5 lost id whose rpkm is not 0. I don't know why the cuffcompare filter some Cufflinks transcript.

[king.carly.j]

I have a similar problem, would love to hear what others think.

Answer 1

[pengchy]

I have checked several tmap file, not found this problem. Are you sure that the cuffcompare run successfully or not finished early? What about rerun cuffcompare?