SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Different fpkm values for cuffdiff and cuffcompare madsaan Bioinformatics 3 12-12-2012 04:14 PM
cufflinks FPKM >>> Cuffdiff FPKM peromhc Bioinformatics 6 10-17-2012 01:07 PM
Cuffcompare/cuffdiff changes FPKM values of same BAM in sequential runs SEQond RNA Sequencing 2 10-17-2011 06:42 AM
cuffcompare - FPKM==0 Boel Bioinformatics 2 03-04-2010 07:49 AM
cuffcompare - FPKM==0 Boel Bioinformatics 0 02-25-2010 04:45 AM

Reply
 
Thread Tools
Old 09-05-2011, 11:20 PM   #1
henning
Junior Member
 
Location: Gent

Join Date: May 2011
Posts: 7
Default Empty FPKM estimates after cuffcompare

I ran cufflinks on several BAM files and get tracking.gtf files looking like (truncated lines):

Code:
Chr1    Cufflinks   transcript  22746   23685   1000    +   .   gene_id "CUFF.8"; transcript_id "CUFF.8.1"; FPKM "32.3697173163"; frac "1.000000"; conf_lo "28.299584"; conf_hi "36.439851"; cov "52.362831";
Chr1    Cufflinks   exon    22746   23020   1000    +   .   gene_id "CUFF.8"; transcript_id "CUFF.8.1"; exon_number "1"; FPKM "32.3697173163"; frac "1.000000"; conf_lo "28.299584"; conf_hi "36.439851"; cov "$
Chr1    Cufflinks   exon    23096   23685   1000    +   .   gene_id "CUFF.8"; transcript_id "CUFF.8.1"; exon_number "2"; FPKM "32.3697173163"; frac "1.000000"; conf_lo "28.299584"; conf_hi "36.439851"; cov "$
Chr1    Cufflinks   transcript  79944   80186   1000    +   .   gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "3077.9273423595"; frac "1.000000"; conf_lo "1765.494714"; conf_hi "4390.359971"; cov "2714.84$
Ch
and then run cuffcompare to compare with a merged gtf file as
Code:
cuffcompare -o myprefix -r merged.gtf transcripts.gtf
but, the myprefix.tracking only gives me FPKM estimates equal zero for all genes:

Code:
TCONS_00000001  XLOC_000001 XLOC_000001|TCONS_00000001  c   q1:CUFF.8|CUFF.8.1|100|0.000000|0.000000|0.000000|0.000000|-
TCONS_00000002  XLOC_000002 XLOC_000002|TCONS_00000002  =   q1:CUFF.11|CUFF.11.1|100|0.000000|0.000000|0.000000|0.000000|-
TCONS_00000003  XLOC_000003 XLOC_000003|TCONS_00000003  =   q1:CUFF.2|CUFF.2.1|100|0.000000|0.000000|0.000000|0.000000|-
TCONS_00000004  XLOC_000004 XLOC_000004|TCONS_00000004  =   q1:CUFF.4|CUFF.4.1|100|0.000000|0.000000|0.000000|0.000000|-
TCONS_00000005  XLOC_000005 XLOC_000005|TCONS_00000006  c   q1:CUFF.16|CUFF.16.1|100|0.000000|0.000000|0.000000|0.000000|-
T
note that CUFF.8 in the transcripts.gtf has a non-zero FPKM estimate but this does not propagate to the myprefix.tracking file.

Any ideas why? Grateful for answers.
henning is offline   Reply With Quote
Old 09-13-2011, 06:58 AM   #2
bgibb
Junior Member
 
Location: San Francisco, CA

Join Date: Jul 2010
Posts: 7
Default

Have you tried running it with Cufflinks-1.1.0? (released last week)

I noticed a similar problem with the .tmap files generated by cuffcompare in release 1.0.3, however that problem seems to have been corrected in the most recent release.
bgibb is offline   Reply With Quote
Old 09-21-2011, 07:53 AM   #3
henning
Junior Member
 
Location: Gent

Join Date: May 2011
Posts: 7
Default

Thanks for the tip, I tried Cufflinks-1.1.0 and indeed this solves the problem!
henning is offline   Reply With Quote
Reply

Tags
cuffcompare, rna-seq

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 09:42 AM.


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