[maker-devel] should EST evidence be cleaned, assembled?

[Carson Holt]

You will want to trim the vector or any sequence not representative of the transcript or else it will not align well. The sequences will be aligned directly against the assembly.

—Carson


> On Sep 22, 2016, at 10:27 AM, Steven Sullivan <sullis02 at nyu.edu> wrote:
> 
> Do EST sequences (as opposed to RNA Seq data) need to be cleaned (e.g., vector sequence trimmed, Ns removed) and assembled (combined into longer 'EST contigs' where possible)  before use as  MAKER alignment evidence?   
> 
> 
> -- 
> Dr. Steven Sullivan
> Center for Genomics & Systems Biology
> New York University
> 12 Waverly Place
> New York, NY 10003
> 
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