SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Allele-specific expression from samtools mpileup data RedMary Bioinformatics 0 07-31-2012 03:35 AM
RNA-Seq: AlleleSeq: analysis of allele-specific expression and binding in a network f Newsbot! Literature Watch 2 10-27-2011 02:13 PM
RNA-Seq: Deterministic and Stochastic Allele Specific Gene Expression in Single Mouse Newsbot! Literature Watch 0 07-07-2011 03:00 AM

Reply
 
Thread Tools
Old 10-09-2013, 07:54 PM   #1
saran.ela123
Junior Member
 
Location: Singapore

Join Date: Aug 2013
Posts: 5
Post Tools for analysis allele specific expression in RNA-Seq data?

Hi all !!!

I am working on arabidopsis thaliana rna seq data. i need to analysis allele specific expression of it. can any body help me to select tool for snp calling and analysis (Allele specific expression).

Thanks in advance
saran.ela123 is offline   Reply With Quote
Old 10-10-2013, 01:54 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

There are a number of tools out there for this sort of thing. For SNP calling, there's GATK or samtools, but also see this recent paper that's one of the few out there to directly look at calling SNPs from RNAseq data. Once you have the SNPs, you again have a few options. Among the published tools (I think most of us have just written our own solutions, it's pretty straight-forward) are AlleleSeq and Allim.
dpryan is offline   Reply With Quote
Reply

Tags
allele distributions, rna-seq data analysis, snp analysis, snp calling

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 10:14 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO