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

[Carson Holt]

Hi Jason,

Assembly based approaches like Trinity have high specificity and lower sensitivity (i.e. low false positive rates but higher false negative rates) while alignment approaches like cufflink have high sensitivity but low specificity  (low false negative rates but high false positive rates).  The low false negative rates of an assembly approach are easily rescued by the protein data supplied to MAKER from a related genome.  But the high false positive rates seen in programs like cufflinks cannot be easily corrected for.  Since MAKER relies on the evidence you give it, the problem basically becomes junk in - junk out.

I would imagine that the genome guided approach for Trinity may increase sensitivity, but I haven’t really explored the differences between the two approaches. As long as it doesn’t generate more false positives, it may be worth a try.

I’ll let Jason Stajich answer the part about PASA.  I don’t use it because of the heavy database backend required, but Brian Haas (PASA developer) said he’s working on a database-less version of PASA that can more easily be integrated into MAKER.  We’ve already integrated one of his other tools (EVM) into the development version of MAKER.

Thanks,
Carson



> On Apr 22, 2015, at 3:04 PM, Jason Gallant <jgallant at msu.edu> wrote:
> 
> 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. Gallant
> Assistant Professor
> Room 38 Natural Sciences
> Department of Zoology
> Michigan State University
> East Lansing, MI 48824
> jgallant at msu.edu
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