Mapping RNA-seq against genome
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
1 answer
TopHat is crazy slow. Try STAR (as iraun mentioned), hisat, hisat2, or even BBMap.
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Devon Ryan
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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.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..
Here are the GATK best practices for variant calling in RNA Seq:
http://gatkforums.broadinstitute.org/firecloud/discussion/3891/calling-variants-in-rnaseq