View Single Post
Old 10-10-2012, 03:16 PM   #1
jay2008
Member
 
Location: Australia

Join Date: Sep 2010
Posts: 44
Default is it bug in cufflinks?

hello,
I run cufflinks and got the following transcripts from transcript.gtf:
chrX Cufflinks transcript 107821319 107840299 1000 + . gene_id "CUFF.33619";transcript_id "CUFF.33619.1"; FPKM "9.8800098066"
...
chrX Cufflinks transcript 107840614 107940873 1000 +chrX Cufflinks transcript 107683040 107816842...
...
chrX Cufflinks transcript 107821319 107840299 1000 + . gene_id "CUFF.33619"; transcript_id "CUFF.33619.1"; FPKM "9.8193962495"

I have several problems:
(1) the middle of the second "1000+chrX", what does it means?
(2) the first and third rows share the same transcript id "CUFF.33619.1". what is the reason to repeat the same transcript?
jay2008 is offline   Reply With Quote