Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Cuffdiff splicing.diff Greg Bioinformatics 1 11-04-2013 05:04 PM
Cuffdiff NOTEST for splicing.diff Greg Bioinformatics 5 11-14-2011 06:22 AM
multiple FPKM problem for single gene in gene_exp.diff after running cuffdiff ngs RNA Sequencing 4 03-30-2011 02:55 PM
Multiple gene entries in cuffdiff output ae_ucla RNA Sequencing 1 10-22-2010 04:54 PM
Gene information in Cuffdiff output files hong_sunwoo Bioinformatics 2 10-05-2010 06:13 AM

Thread Tools
Old 02-13-2011, 12:30 AM   #1
Location: Israel

Join Date: Oct 2010
Posts: 19
Default multiple lines per single gene in gene_exp.diff output of cuffdiff

question that was posted on another forum, maybe someone here will have an answer:

after running cuffdiff, in the gene_exp.diff file there are multiple lines for the same gene, with different FPKM values.
any idea for the cause or how should I handle this to receive a single value per gene?

reut is offline   Reply With Quote
Old 02-14-2011, 05:12 AM   #2
Location: Bethesda, MD

Join Date: Apr 2009
Posts: 51


Have you gone back to your something.combined.gtf file to look up the entry by XLOC value?

I assumed that this was a bug and wrote a little program that compares the gene_exp.diff file and the combined.gtf and fixes the locus field in gene_exp.diff to what it should be based on the gtf file.

Has anyone else had any experience with this?

sdarko is offline   Reply With Quote
Old 03-09-2015, 05:16 AM   #3
Location: Pittsburgh, PA

Join Date: May 2010
Posts: 22
Default Multiple entries of a gene/locus at Cuffdiff Differential Gene Expression Output


I'm also getting this probelm (gene_exp.diff):

XLOC_021564 Hnf4a 3:165976692-166162683
XLOC_022796 Hnf4a 3:165976692-166162683
XLOC_022797 Hnf4a 3:165976692-166162683

When I looked at isoform_exp.diff file for Hnf4a all the mentioned isoforms like in the same region 3:165976692-166162683, but seem to be distributed among the above locus ids such that no locus id above share any isoform:
test_id gene_id gene locus
TCONS_00057332 XLOC_021564 Hnf4a 3:165976692-166162683
TCONS_00057337 XLOC_021564 Hnf4a 3:165976692-166162683
TCONS_00057338 XLOC_021564 Hnf4a 3:165976692-166162683
TCONS_00057339 XLOC_021564 Hnf4a 3:165976692-166162683
TCONS_00057340 XLOC_021564 Hnf4a 3:165976692-166162683
TCONS_00057341 XLOC_021564 Hnf4a 3:165976692-166162683
TCONS_00057342 XLOC_021564 Hnf4a 3:165976692-166162683
TCONS_00060713 XLOC_022796 Hnf4a 3:165976692-166162683
TCONS_00060714 XLOC_022797 Hnf4a 3:165976692-166162683
TCONS_00060715 XLOC_022797 Hnf4a 3:165976692-166162683

My pipeline:

Gsnap (Reference guided Mapping, default settings) --> Remove softclip bases (script shared by rna-star author Alexander Dobin) --> Cufflinks (Reference guided; default settings) --> Cuffmerge (all samples cufflinks transcript.gtf + reference.gtf) --> Cuffdiff (default settings)

The reason to remove soft-clip bases prior to running cufflinks is to have compatibility of Gsnap mapping output with Cufflinks because cufflinks uses soft-clipped bases to do assembly leading to assembled transcripts sometimes beyond reference length and throws an error at Cuffmerge. For more info on this!

Right now I am re-running the above pipeline with TopHat but I don't think it will solve this problem, because the problem is at cuffmerge, I think, in deciding to include some transcript/isoform assembly under one locus id and some in the other, within the same locus region, leading to redundancy in locus region and gene enteries.

This is not for 1 gene above. Overall in gene_exp.diff file:

Out of 25667 genes 3776 are repeated
Out of 23862 loci positions (format: chr:start-end) 5759 are repeated.

That's a significant number of genes have multiple entries.

Did anyone else have this problem as well?

Cufflinks version I used: cufflinks/2.2.1
Genome: Rat genome rn5 (Ensembl db)
Reference gtf of genes: Ensembl database version 77 for rn5


Last edited by rahilsethi; 03-09-2015 at 05:29 AM.
rahilsethi is offline   Reply With Quote

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 01:50 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO