SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Differential expression, splicing, and promoter use with Cufflinks Cole Trapnell Bioinformatics 47 09-24-2015 03:03 PM
Cufflinks differential expression problem Rachelly Bioinformatics 2 05-11-2011 11:08 PM
Differential gene expression: Can Cufflinks/Cuffcompare handle biological replicates? marcora Bioinformatics 38 12-14-2010 03:57 PM
Differential gene expression of gene clusters anjana.vr RNA Sequencing 1 10-28-2010 10:33 AM
Differential gene expression: Can Cufflinks/Cuffcompare handle biological replicates? marcora Bioinformatics 0 05-19-2010 01:11 AM

Reply
 
Thread Tools
Old 11-21-2010, 09:33 PM   #1
waterboy
Member
 
Location: India

Join Date: Oct 2010
Posts: 14
Default help with differential gene expression with cufflinks and tophat

Hi All,
We are looking for differential gene expression of two different samples of the same species.

After running tophat, for two different samples of the same species, we got accepted_hits.bam files for both. Then we ran cufflinks with the following command for both of the samples:

$./cufflinks -G refGene.gtf accepted_hits1.bam
$./cufflinks -G refGene.gtf accepted_hits2.bam
where refGene.gtf is the main gtf file of the species downloaded from UCSC.

This provided us with three files, genes.expr, transcripts.expr, transcripts.gtf (for two samples, all in all, we got 6 files, genes1.expr, transcripts1.expr, transcripts1.gtf, genes2.expr, transcripts2.expr, transcripts2.gtf)

Then, we carried out cuffcompare with the following command but we are not quite sure as to this is the right way to do it or not.

$./cuffcompare -r refGene.gtf /sample1/transcripts1.gtf /sample2/transcripts2.gtf (Is this how it should be?)

Output: stdout.combined.gtf, stdout.loci, stdout.tracking

Then we carried out cuffdiff with the following command but we are not quite sure as to this is the right way to do it or not.

$./cuffdiff stdout.combined.gtf accepted_hits1.bam accepted_hits2.bam (Is this how it should be?)


Now we want to do the differential gene expression for which we guess we need to use cuffcompare and cuffdiff, right? It will be highly appreciated if anyone can guide us on the same. Also, please tell us as to what files would be input for cuffcompare and cuffdiff to do the differential gene expression.

Thank you very much for the helping hand.
waterboy is offline   Reply With Quote
Old 11-28-2010, 09:51 AM   #2
adarob
Member
 
Location: Berkeley, CA

Join Date: Jul 2010
Posts: 71
Default

Your commands appear to be correct.
adarob 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 01:02 AM.


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