[maker-devel] annotation comparison aed plots

[Michael Campbell]

Hi Robert,

Here are the scripts that were mentioned before.

The AED_cdf_generator.pl script is for making cumulative distribution
function plots based on annotation edit distance. This script is quite
simple and strait forward in its internals.

The compare_annotations_3.2.pl script is for generating summary stats for
annotations and will compare two annotations of the same assembly.

You can run either script without arguments to get a usage statement.

Thanks,
Mike


On Mon, Mar 10, 2014 at 6:17 AM, Robert King (RRes-Roth) <
robert.king at rothamsted.ac.uk> wrote:

>  Dear Maker Developers,
>
>
>
> I've updated a reference that was had errors and was a little incomplete
> and now trying to produce a annotation for it. Please note the reference
> has not changed dramatically. I've produced two annotations using as
> evidence:
>
>
>
> Annotation 1:
>
> Uniprot proteins search using species keyword "fusarium"
>
> Pubmed mRNA for the name of the organism
>
> Prior annotation reference transcripts
>
>
>
> Annotation 2:
>
> Uniprot proteins search using species keyword "fusarium"
>
> Pubmed mRNA for the name of the organism
>
> Prior annotation reference transcripts
>
> mRNA trinity assembly pasafly of different strain (only RNA-seq available)
>
>
>
> I'm not sure if it was a smart move to use the prior annotation reference
> transcripts?
>
>
>
> I want to compare these two annotations and have produced AED scores. How
> do I generate summary stats/figures to compare annotations. You mentioned
> last year in a post Mike Campbell has a script to produce these, do you
> know if he will post it? I've got the Eval program and converted to gtf
> format using the provided script, just waiting on some perl modules to be
> installed by admin to test it. I'm waiting on some perl modules to be
> installed by our administrator to test out the "Evaluator" and "compare"
> programs too, what do they do?
>
>
>
> Best Wishes
>
> Rob
>
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>


-- 
Michael Campbell MS, RD.
Doctoral Candidate
Eccles Institute of Human Genetics
University of Utah
15 North 2030 East, Room 2100
Salt Lake City, UT 84112-5330
ph:585-3543
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