Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
.gtf or .gff file for TopHat and Cufflinks (and bowtie2) rubbertjes Bioinformatics 11 08-07-2013 06:31 PM
Cufflinks Duplicate GFF ID: will it affect the result? byb121 Bioinformatics 2 07-15-2013 04:10 PM
cufflinks, gff and bam order kenietz RNA Sequencing 0 09-16-2012 07:29 PM
Convert cufflinks GTF to GFF seq_newbie Bioinformatics 2 07-09-2011 05:54 AM
cufflinks -G gff/gtf format guangxiwu Bioinformatics 0 04-22-2011 09:43 AM

Thread Tools
Old 05-22-2014, 07:31 PM   #1
Junior Member
Location: Australia

Join Date: Apr 2014
Posts: 4
Default Question: Cufflinks, without GFF-error

Dear All SeqUser

Me and my colleague are working with RNA-seq data and each of us got the same problem, using cufflinks.

First what I did:

tophat2 without gff file (because if I used the gff file, the cufflinks was taking and calculating the FPKM for genome-genes_corrdinates.gff without short reads mapped there.

and after I tried to run the cufflinks like that:

cufflinks -p 8 -o cufflinks accepted_hits.bam

and I got NOTHING.

You are using Cufflinks v2.2.1, which is the most recent release.
[12:07:28] Inspecting reads and determining fragment length distribution.

> Processed 1 loci. [*************************] 100%
> Map Properties:
> Normalized Map Mass: 68.00
> Raw Map Mass: 68.00
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[12:07:28] Assembling transcripts and estimating abundances.

> Processed 0 loci. [*************************] 100%

I tried to find the solution here in and also on other website but what I only found was that maybe we don't have enough RAM but for sure we have enough. We are using big server.

Could someone help me (us)? What is wrong and how to solve the problem?

I am running out of time and still I don't know how to run the cufflinks to get the results


dodo1981 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 11:41 AM.

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