SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



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
Empty FPKM estimates after cuffcompare henning RNA Sequencing 2 09-21-2011 07:53 AM
cuffcompare - FPKM==0 Boel Bioinformatics 0 02-25-2010 04:45 AM

Reply
 
Thread Tools
Old 02-23-2010, 07:45 AM   #1
Boel
Member
 
Location: Stockholm, Sweden

Join Date: Oct 2009
Posts: 62
Default cuffcompare - FPKM==0

Dear All,

I'm playing around with cufflinks, and just realized that most of my FPKM values are zero in my .tmap files although the confidence interval is != 0.

> grep TCONS_00000051 transcripts.tmap
USP14 TCONS_00000051 i CUFF.167867 CUFF.167867.0 100 0.000000 2.633003 13.165017 6.534247 146 CUFF.167867.0
USP14 TCONS_00000051 i CUFF.167870 CUFF.167870.0 100 0.000000 2.309612 13.461403 6.523077 130 CUFF.167870.0
USP14 TCONS_00000051 i CUFF.167873 CUFF.167873.0 100 0.000000 1.684046 12.115592 5.300000 130 CUFF.167873.0
USP14 TCONS_00000051 i CUFF.167876 CUFF.167876.0 100 0.000000 44.074354 96.153772 29.000000 53 CUFF.167876.0
USP14 TCONS_00000051 i CUFF.167879 CUFF.167879.0 100 0.000000 8.646888 24.069578 13.531915 141 CUFF.167879.0
USP14 TCONS_00000051 i CUFF.167882 CUFF.167882.0 100 0.000000 28.206807 50.772252 32.666667 159 CUFF.167882.0
USP14 TCONS_00000051 i CUFF.167885 CUFF.167885.0 100 0.000000 10.328430 17.438920 11.484902 563 CUFF.167885.0
USP14 TCONS_00000051 i CUFF.167888 CUFF.167888.0 100 0.000000 9.756814 22.765900 13.182741 197 CUFF.167888.0
USP14 TCONS_00000051 i CUFF.167891 CUFF.167891.0 100 0.000000 25.562775 42.429610 27.689796 245 CUFF.167891.0

In the transcripts.gtf files from cufflinks all exons have FPKM values.

This is the cuffcompare code I ran:
cuffcompare -r /path/NCBI36.combined.gtf -R tophat_Y1_100216/transcripts.gtf tophat_Y2_100215/transcripts.gtf tophat_Y3_100216/transcripts.gtf tophat_Y4_100215/transcripts.gtf

I'm using cufflinks-0.8.1.
The reference gtf file (NCBI36.combined.gtf) was built from ensembl annotation (Homo_sapiens.NCBI36.48.gtf), where tss_ids were created using:
"cuffcompare -r reference.gtf reference.gtf reference.gtf"

Any ideas as to what might have gone wrong here?

Thanks,
Boel
Boel is offline   Reply With Quote
Old 03-03-2010, 05:26 PM   #2
Ichinichi
Member
 
Location: Philadelphia

Join Date: Mar 2010
Posts: 10
Default

Quote:
Originally Posted by Boel View Post
Dear All,

I'm playing around with cufflinks, and just realized that most of my FPKM values are zero in my .tmap files although the confidence interval is != 0.

> grep TCONS_00000051 transcripts.tmap
USP14 TCONS_00000051 i CUFF.167867 CUFF.167867.0 100 0.000000 2.633003 13.165017 6.534247 146 CUFF.167867.0
USP14 TCONS_00000051 i CUFF.167870 CUFF.167870.0 100 0.000000 2.309612 13.461403 6.523077 130 CUFF.167870.0
USP14 TCONS_00000051 i CUFF.167873 CUFF.167873.0 100 0.000000 1.684046 12.115592 5.300000 130 CUFF.167873.0
USP14 TCONS_00000051 i CUFF.167876 CUFF.167876.0 100 0.000000 44.074354 96.153772 29.000000 53 CUFF.167876.0
USP14 TCONS_00000051 i CUFF.167879 CUFF.167879.0 100 0.000000 8.646888 24.069578 13.531915 141 CUFF.167879.0
USP14 TCONS_00000051 i CUFF.167882 CUFF.167882.0 100 0.000000 28.206807 50.772252 32.666667 159 CUFF.167882.0
USP14 TCONS_00000051 i CUFF.167885 CUFF.167885.0 100 0.000000 10.328430 17.438920 11.484902 563 CUFF.167885.0
USP14 TCONS_00000051 i CUFF.167888 CUFF.167888.0 100 0.000000 9.756814 22.765900 13.182741 197 CUFF.167888.0
USP14 TCONS_00000051 i CUFF.167891 CUFF.167891.0 100 0.000000 25.562775 42.429610 27.689796 245 CUFF.167891.0

In the transcripts.gtf files from cufflinks all exons have FPKM values.

This is the cuffcompare code I ran:
cuffcompare -r /path/NCBI36.combined.gtf -R tophat_Y1_100216/transcripts.gtf tophat_Y2_100215/transcripts.gtf tophat_Y3_100216/transcripts.gtf tophat_Y4_100215/transcripts.gtf

I'm using cufflinks-0.8.1.
The reference gtf file (NCBI36.combined.gtf) was built from ensembl annotation (Homo_sapiens.NCBI36.48.gtf), where tss_ids were created using:
"cuffcompare -r reference.gtf reference.gtf reference.gtf"

Any ideas as to what might have gone wrong here?

Thanks,
Boel
I have this exact same problem. Any help?
Ichinichi is offline   Reply With Quote
Old 03-04-2010, 07:49 AM   #3
Boel
Member
 
Location: Stockholm, Sweden

Join Date: Oct 2009
Posts: 62
Default Bug

Apparently this is a bug, and Cole & CO is currently working on solving it for the new release that should come out in the near future. Haven't heard anything more yet.
Boel 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 10:10 PM.


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