Using CEGMA to build HMM

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Using CEGMA to build HMM

Amal MOHSINE
Hi,
I chose CEGMA to identify an initial gene set in order to model the HMM
but the gff file from CEGMA output has as tags "First, Internal, Terminal", not "mRNA, CDS" as expected by maker2zff.pl
so when I try to convert my gff file to zff using maker2zff, I get errors.
Is there a way to convert CEGMA output into snap ZFF format?
Many thanks,
Amal


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Re: Using CEGMA to build HMM

Carson Hinton Holt
Re: [maker-devel] Using CEGMA to build HMM So cegma output is in GTF format technically and not GFF3 which is why the maker2zff script will not run on it.  In MAKER 2.0 which was recently posted online, there is a script called cegma2zff that will do that conversion for you.

Thanks,
Carson


On 6/10/10 5:36 AM, "Amal MOHSINE" <amal_mh@...> wrote:

Hi,
I chose CEGMA to identify an initial gene set in order to model the HMM
but the gff file from CEGMA output has as tags "First, Internal, Terminal", not "mRNA, CDS" as expected by maker2zff.pl
so when I try to convert my gff file to zff using maker2zff, I get errors.
Is there a way to convert CEGMA output into snap ZFF format?
Many thanks,
Amal
       

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