SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Error at Creating Count Table for DESeq2 sazz Bioinformatics 2 11-11-2014 03:52 AM
Question for making count table for edgeR lucer105 Bioinformatics 3 12-13-2013 07:01 AM
What to include in my count table(s) for DESeq rndouglas Bioinformatics 5 11-08-2013 05:54 AM
Count table from BAM file with custom gtf tamari Bioinformatics 3 09-05-2013 02:42 PM
Alternative to cufflinks? - Bam to count table? hbt Bioinformatics 3 11-09-2012 06:09 AM

Reply
 
Thread Tools
Old 08-26-2014, 03:12 AM   #1
ahmadsam
Junior Member
 
Location: best

Join Date: Dec 2011
Posts: 9
Question How to create count table for SOAP output?

Hi
I would like to use SOAP to align RNA-Seq reads with Rice genome, i have 2 questions :

1- How can i use GTF gene annotation file in SOAP ? (and which version?)
2-How can i create Count table for SOAP output (any software) ?

thanks
ahmadsam is offline   Reply With Quote
Old 08-26-2014, 08:51 AM   #2
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

Soap is not designed for RNA-seq alignment, and it does not use GTF files. You'd be better off using a splice-aware aligner such as BBMap, TopHat, or Star.

For determining gene expression, many people use Cufflinks.
Brian Bushnell 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 02:21 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO