Mapping RNA-seq against genome
1
2
Entering edit mode
5.8 years ago
User000 ▴ 490

Hello,

I have RNA-seq data of several varieties from the same plant species. I also have a genome from, let's say, ancestor of that species, which I am going to use as a reference. I am interested in studying SNPs (Single Nucleotide Polimorphisms). Which aligner do you suggest me to use in order to map my RNA-seq data to the reference genome? I am thinking to go for TopHat.

Also, could you suggest some pipeline to do this kind of analyses?

P.S. there is a problem of homoeologous genomes in my plant species

RNA-Seq SNP • 2.8k views
ADD COMMENT
2
Entering edit mode

I'd suggest you to give a try to STAR. It is much faster than tophat, though it consumes a considerable amount of RAM. So, having enough computer power, I'd definitely use STAR.

ADD REPLY
0
Entering edit mode

Thanks for your reply.I have a problem with a computer RAM, basically I want to try to use on a normal computer 1st to see if it works, if no I will have to seek for a server..

ADD REPLY
0
Entering edit mode

Here are the GATK best practices for variant calling in RNA Seq:

http://gatkforums.broadinstitute.org/firecloud/discussion/3891/calling-variants-in-rnaseq

ADD REPLY
4
Entering edit mode
5.8 years ago

TopHat is crazy slow. Try STAR (as iraun mentioned), hisat, hisat2, or even BBMap.

ADD COMMENT

Login before adding your answer.

Traffic: 2575 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6