SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Cufflinks / Cuffdiff problem Morten Bioinformatics 42 07-13-2013 10:51 PM
Cufflinks/Cuffdiff...what next? nsl Bioinformatics 0 06-20-2011 07:41 AM
Cufflinks then Cuffdiff plefebvre RNA Sequencing 1 04-20-2011 05:56 AM
Cufflinks, Cuffdiff and annotation chrisbala RNA Sequencing 8 04-05-2011 03:10 PM
transcripts by cufflinks and cuffdiff mrfox Bioinformatics 1 11-22-2010 05:44 PM

Reply
 
Thread Tools
Old 11-10-2011, 02:03 PM   #1
snape_ar
Junior Member
 
Location: Seattle

Join Date: Oct 2011
Posts: 5
Default Cufflinks and CuffDiff

I have 2 RNA-Seq biological replicates and I ran Tophat and then Cufflinks on it separately for both samples. The outputs of Cufflinks for each replicates are:

Replicate 1:
1. transcript.gtf file
2. genes.fpkm_tracking
3. isoform.fpkm_tracking

Replicate 2:
1. transcript.gtf file
2. genes.fpkm_tracking
3. isoform.fpkm_tracking

I would like to compare the differential expression between the two biological replicates by running CuffDiff. So, my question is when I am running the following command:

cuffdiff [options]* <transcripts.gtf> <sample1_replicate1.sam[,...,sample1_replicateM]> <sample2_replicate1.sam[,...,sample2_replicateM.sam]>... [sampleN.sam_replicate1.sam[,...,sample2_replicateM.sam]]

What should be my transcripts.gtf file ? Is it the combination of the two transcripts.gtf files or is it of replicate 1/2 ?

Thanks.
snape_ar is offline   Reply With Quote
Old 11-10-2011, 05:28 PM   #2
Nicolas
Member
 
Location: new york city

Join Date: Apr 2009
Posts: 40
Default

I used the annotation files used in Tophat/Cufflinks but your question makes me realize that this is confusing. The manual page says:
"<transcripts.(gtf/gff)> A transcript annotation file produced by cufflinks, cuffcompare, or other source."

but the How to start page (http://cufflinks.cbcb.umd.edu/tutori...l#differential) says:
cuffdiff annotation.gtf mock_rep1.bam,mock_rep2.bam \
knockdown_rep1.bam,knockdown_rep2.bam

I had good results with the annotation file, but I probably missed the novel transcripts. If that's what you're after, you should merge the 2 transcript.gtf and run cuffdiff with it.
Nicolas is offline   Reply With Quote
Old 11-10-2011, 08:04 PM   #3
jbrwn
Member
 
Location: Denver, CO

Join Date: Mar 2011
Posts: 37
Default

what nicolas said. use cuffmerge to merge the two *.gtf files from cufflinks output.
jbrwn 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 06:50 AM.


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