SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Using edgeR to compare a pair of genomic features between many samples agolson1 Bioinformatics 0 12-30-2014 01:55 PM
Is it possible to do DE analysis on single tumor-normal pair with EdgeR? ymc RNA Sequencing 3 07-28-2013 12:52 AM
Public gene prediction GTFs for human rboettcher Bioinformatics 0 07-01-2013 01:30 AM
Cuffmerge: merging reference and transcript GTFs? mra Bioinformatics 0 06-27-2013 11:08 AM
mate pair + single read data boetsie General 1 04-14-2010 09:08 AM

Reply
 
Thread Tools
Old 02-10-2016, 11:20 AM   #1
nimrod337
Member
 
Location: Wisconsin

Join Date: Jun 2013
Posts: 22
Default cuffmerge all gtfs to use in single pair compare?

Hey all, I couldn't find anything using the search function, so I'll just ask here. If this is the wrong spot, please feel free to move, or tell me where it should be posted.

Question is this: I have 2 varieties of rice, treated at 3 time points, and untreated at time=0. 3 bio reps for each "treatment". I ran cufflinks, and got .gtf files for each treatment. then used cuffmerge to put all 24 treatments into a single "super.gtf". Can I use this super.gtf in cuffdiff if I am only going to compare two samples? Or should I use cuffmerge to merge those two samples' gtf files, and use that specific combined.gtf in my cuffdiff command? It would be nice if I could just use the "super.gtf" for all my comparisons.

Thanks!
nimrod337 is offline   Reply With Quote
Old 02-10-2016, 07:48 PM   #2
harrike
Member
 
Location: St. Louis, MO

Join Date: Jun 2010
Posts: 29
Default

Hi nimrod337,

If I was you, I would just use the "super.gtf". First, the cuffmerged (from 24 samples) super.gtf gives you the most complete transcript annotation, which should include all the annotations coming from combination of any two samples. Second, technically it will become complicated if you cuffmerge every two samples separately, as each time different ID may be given to the same gene in the genome, that is, the same gene will be assigned with different names in different .gtf files. How to keep the name consistent will be a headache.

Cheers,

Rui
harrike is offline   Reply With Quote
Old 02-10-2016, 07:54 PM   #3
nimrod337
Member
 
Location: Wisconsin

Join Date: Jun 2013
Posts: 22
Default

Awesome. That's what I was hoping someone would say. I imagined the individual merging would be a serious pain, but I was willing to do it, if it was the proper way. I just fired off the cuffdiff commands, and haven't seen any errors yet!! Thanks again,
A
nimrod337 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 08:47 PM.


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