[maker-devel] Best way to assemble RNA-seq for MAKER

[Carson Holt]

I would pool them.  You will get better coverage of low expression transcripts.  While there may be differently spliced transcripts among the tissues, MAKER and all gene prediction programs used by MAKER by default are not going to try and work out alternate splicing anyways.  You can tell it to (altsplice= option), but your EST evidence has to be near perfect end-to-end for that to work.

—Carson


> On Jun 29, 2015, at 4:45 PM, John Cornelius <jcornel3 at asu.edu> wrote:
> 
> Hi I have a quick question, I have RNA-seq from several different tissue types and I was wondering, would it be better to pool them and assemble them as one large transcriptome? Or, should I assemble each tissue separately and then use MAKER to integrate the smaller assemblies into the annotation? Thanks.
> 
> -- 
> John Cornelius
> MCB PhD Candidate
> Arizona State University
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org