[maker-devel] annotation comparison aed plots

[Michael Campbell]

One more point. The sensitivity, specificity,and accuracy produced by the
compare_annotations_3.2.pl script are gene level, and overlap is defined
very liberally between annotation sets is defined as at least one
nucleotide of an exon overlap.
Mike


On Mon, Mar 10, 2014 at 9:47 AM, Michael Campbell <
michael.s.campbell1 at gmail.com> wrote:

> 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
>
>


-- 
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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