[maker-devel] maker-devel Digest, Vol 92, Issue 1

[张志斌]

Hi every one <br/>I wonder where I can downlaod the perl package proc::signal? I can not find it in CPAN. who could send me the package or give me the website where i can get it ?<br/><br/>thans for your help
At 2016-01-02 03:00:02, maker-devel-request at yandell-lab.org wrote:
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>Today's Topics:
>
>   1. running MAKER to merge annotations (Arun Seetharam)
>   2. Re: running MAKER to merge annotations (Daniel Ence)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Fri, 1 Jan 2016 12:31:06 -0600
>From: Arun Seetharam <arnstrm at gmail.com>
>To: maker-devel at yandell-lab.org
>Subject: [maker-devel] running MAKER to merge annotations
>Message-ID:
>	<CAF21SX7fJ2fktyV_pu4wfs4x2wYGgc-uiRdTJm9ZdRu_JrhiZQ at mail.gmail.com>
>Content-Type: text/plain; charset="utf-8"
>
>Hi all,
>
>First of all, a very happy new year to all of you! I hope everyone is
>having a great holiday season.
>
>I have a question about Maker. For my grass species, I ran 3 separate
>rounds of MAKER (low GC, regular GC and high GC) and I now have 3 maker gff
>files. So, what is the correct way to merge these files to a single gff
>file? Do I have to run a maker round with just the GFF files as input? It
>looks like EVM especially meant to do this kind of job, but not sure if
>Maker does this too.
>
>Thanks for any help or suggestions!
>
>Have a nice day,
>-- 
>Arun Seetharam
>Post Doctoral Research Associate
>Genome Informatics Facility & EEOB
>Office of Biotechnology
>228 Science I
>Iowa State University
>Ames, Iowa 50011
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>------------------------------
>
>Message: 2
>Date: Fri, 1 Jan 2016 18:37:38 +0000
>From: Daniel Ence <dence at genetics.utah.edu>
>To: Arun Seetharam <arnstrm at gmail.com>
>Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>Subject: Re: [maker-devel] running MAKER to merge annotations
>Message-ID: <E9AAB7FC-AF52-45FE-B737-1CED1BD9D4BF at genetics.utah.edu>
>Content-Type: text/plain; charset="utf-8"
>
>Hi Arun, are the three rounds of maker on different parts/versions of the genome or did you maker on the same genome with three different settings? If it?s the former, then you can merge the maker gff files with gff3_merge, which is included with your maker installation. 
>
>If it?s the latter case then I do think EVM could help if you want to give the different result sets different confidence weights. If you want to give them all the same weight, then you could do another run of maker, and pass them through as either models or predictions.
>
>~Daniel
>
>
>
>
>
>Daniel Ence
>Graduate Student
>Eccles Institute of Human Genetics
>University of Utah
>15 North 2030 East, Room 2100
>Salt Lake City, UT 84112-5330
>
>> On Jan 1, 2016, at 11:31 AM, Arun Seetharam <arnstrm at gmail.com> wrote:
>> 
>> Hi all,
>> 
>> First of all, a very happy new year to all of you! I hope everyone is having a great holiday season.
>> 
>> I have a question about Maker. For my grass species, I ran 3 separate rounds of MAKER (low GC, regular GC and high GC) and I now have 3 maker gff files. So, what is the correct way to merge these files to a single gff file? Do I have to run a maker round with just the GFF files as input? It looks like EVM especially meant to do this kind of job, but not sure if Maker does this too.
>> 
>> Thanks for any help or suggestions!
>> 
>> Have a nice day,
>> -- 
>> Arun Seetharam
>> Post Doctoral Research Associate
>> Genome Informatics Facility & EEOB
>> Office of Biotechnology
>> 228 Science I
>> Iowa State University
>> Ames, Iowa 50011
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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>------------------------------
>
>End of maker-devel Digest, Vol 92, Issue 1
>******************************************