[maker-devel] General question about RNA evidence

[Steven Sullivan]

The MAKER documentation I can access (wiki turorials) seems somewhat out of
date as regards RNA evidence , as it focuses a lot on ESTs, whereas today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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