[maker-devel] General question about RNA evidence

[Carson Holt]

You need to assemble the reads using something like Trinity. The assembled results can be aligned to the proper strand with much greater specificity using splice aware alignments. Use the jaccard index options when running Trinity.

—Carson


> On Sep 7, 2016, at 3:04 PM, Steven Sullivan <sullis02 at nyu.edu> wrote:
> 
> The MAKER documentation I can access (wiki turorials) seems somewhat out of date as regards RNA evidence , as it focuses a lot on ESTs, whereas today RNA seq data would likely be more common.  
> 
> So a general question I have is, for a new eukaryotic organism with no models, is it better to use assembled RNA seq reads (i.e., putative transcripts generated by Trinity) as input to 1) ab initio predictors and as 2) MAKER alignment evidence, or is it better to use the reads themselves, unassembled? 
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