[maker-devel] RNAseq - Question for Carson and Jason Staijch

[Jason Gallant]

Hi Carson and Jason,


I’ve heard you guys say several times on this list serve that Trinity is the preferable option for ESTs (vs. Cufflinks). Does this mean the genome-guided or the strict denovo approach?


Second, Jason has mentioned using PASA for generating a “best set of annotations” for use in Augustus training.  I have seen his post (and repost) of this, however there aren’t many details on how to use PASA to accomplish this.  Any chance that you could post a more detailed walkthrough on how to approach this?


Best,
Jason Gallant

—
Dr. Jason R. GallantAssistant Professor
Room 38 Natural Sciences
Department of Zoology
Michigan State University
East Lansing, MI 48824
jgallant at msu.edu

office: 517-884-7756
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