SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
GTF file with gene name attribute for Cuffcompare ChrisL Bioinformatics 15 04-15-2013 08:21 AM
GTF file with one line per gene? cnyh RNA Sequencing 3 03-06-2013 09:36 AM
GTF file from UCSC with Gene name??? golharam General 2 09-17-2012 12:28 PM
entamoeba histolytica reference genome (gene annotation file) in GTF format paula123 Bioinformatics 1 06-04-2012 03:39 AM
tophat -G gene model annotations GTF format? silin284 Bioinformatics 15 04-21-2011 07:26 AM

Reply
 
Thread Tools
Old 03-19-2013, 09:53 AM   #1
mehtaaditya
Junior Member
 
Location: India

Join Date: Mar 2013
Posts: 9
Default how to run tophat without gtf file and annotate the gene

Hi everyone..
i m working on RNA seq data. i dont have ref genome for my RNA seq data. i have CDS as reference genome file for my referenced. i want to run tophat on the same. how can i run tophat without gtf/gff file. after mapping with tophat how i annonate my gene/transcript covered in mapping and differentially expressed in cuffdiff pipeline. how can i annotate it without reference gtf file ?? can someone help me? Any suggestions are Appreciate. Thanks in advance.
mehtaaditya 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 09:35 PM.


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