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-   -   is it bug in cufflinks? (http://seqanswers.com/forums/showthread.php?t=24001)

jay2008 10-10-2012 03:16 PM

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?


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