SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bug? duplicated genes in cufflinks output genes.expr silin284 Bioinformatics 3 05-17-2014 11:19 PM
Cufflinks 0.9.2 BAM bug? kopi-o Bioinformatics 38 05-21-2013 01:47 PM
tophat 1.3.0 bug?? peromhc Bioinformatics 16 06-18-2011 03:12 AM
Cufflinks/cuffdiff: is this a bug? PFS Bioinformatics 3 03-29-2011 07:01 AM
Tophat Bug? jling Bioinformatics 0 02-11-2010 03:14 PM

Reply
 
Thread Tools
Old 10-10-2012, 02:16 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
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:53 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO