SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
CummeRbund questions glados Bioinformatics 15 07-10-2017 03:13 AM
Some cummeRbund questions rvaerle RNA Sequencing 61 02-25-2015 05:01 AM
cummeRbund get isoforms paolo.kunder Bioinformatics 6 04-23-2014 08:59 AM
Galaxy -> cummeRbund How? ekimmike Bioinformatics 4 10-30-2013 01:19 AM
cummeRbund installation m_elena_bioinfo Bioinformatics 3 08-02-2012 02:42 AM

Reply
 
Thread Tools
Old 05-25-2012, 02:45 PM   #1
veber
Junior Member
 
Location: USA

Join Date: May 2012
Posts: 4
Default How to name samples in CummeRbund?

Hello,

Problem: I cannot figure out which sample is which in Cummerbund or how to name them.

Details:
I used Galaxy to run Cufflinks, Cuffmerge, and Cuffdiff. I then downloaded files, renamed them to Cufflinks convention and am trying to visualize my data with CummeRbund in RStudio. I cannot figure out which sample is which and how to name them. For example, my density plot just shows samples as q1, q2.

Can someone please help me out?
veber is offline   Reply With Quote
Old 05-25-2012, 04:49 PM   #2
veber
Junior Member
 
Location: USA

Join Date: May 2012
Posts: 4
Default

It seems possible that the only way to do this is to rename sample names from Sample1/q1, Sample2/q2, etc. in cuffdiff output. I understand from Cufflinks manual that the first sample input into cuffdiff is Sample1/q1 and the second is Sample2/q2.

For example,

285: control.bam
287: test.bam
414: cuffmerge.gtf

425: Cuffdiff on data 285, data 287, and data 414: transcript FPKM tracking

Output
Sample 1= q1 = 285 = control.bam
Sample 2 = q2 = 287 = test. bam

Can someone confirm this and touch on whether this is normal workflow? Is there a way to enable Galaxy to keep original sample names?

Last edited by veber; 05-25-2012 at 05:40 PM.
veber is offline   Reply With Quote
Old 05-27-2012, 04:54 PM   #3
veber
Junior Member
 
Location: USA

Join Date: May 2012
Posts: 4
Default

*Bump

Anyone?
veber is offline   Reply With Quote
Old 05-28-2012, 12:25 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,479
Default

N.B. I'm not familiar with Galaxy. Cuffdiff will set q1/q2 in the order of the files given to it. That is, if you execute "cuffdiff OPTIONS transcripts.gtf control.bam test.bam" or similar then control is usually q1. In the future, use the "-L Label1,Label2,..." switch to make your life easier. I would assume there's a way to do that in Galaxy.
dpryan is offline   Reply With Quote
Old 12-08-2014, 05:10 AM   #5
lechu502
Junior Member
 
Location: Bcn

Join Date: Aug 2010
Posts: 4
Default sed replacment

If you run the experiment with several samples

ie. cuffdiff -o cuffdiff/all REF.gff SAMPLE1.bam,SAMPLE1a.bam,SAMPLE1b.bam SAMPLE2.bam,SAMPLE2a.bam,SAMPLE2b.bam SAMPLE3.bam,SAMPLE3a.bam,SAMPLE3b.bam

you can rename them by entering cuffdiff output directory and running:

sed -i.bak -e 's/q1/SAMPLE1/g;s/q2/SAMPLE2/g;s/q3/SAMPLE3/g' *.diff *.info *_tracking
lechu502 is offline   Reply With Quote
Reply

Tags
cuffdiff, cufflinks, cummerbund, rna-seq

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 10:09 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO