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Old 10-10-2012, 02:16 PM   #1
Location: Australia

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

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?
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