Names/IDs from pred_gff are included in final gff

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Names/IDs from pred_gff are included in final gff

Ole Kristian Tørresen-2
Hi,
as far as I can see, names or IDs of features in gffs given to pred_gff is included in the final output as the name of the feature. As far as I can understand, this is not expected behaviour (it is for model_gff). This is with MAKER 2.31.9.

I have these settings:
map_forward=0
keep_preds=1

I thought that map_forward had to be 1 to get the names for the old GFFs. Can you replicate this?

Thank you.

Sincerely,
Ole K. Tørresen

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Re: Names/IDs from pred_gff are included in final gff

Carson Holt-2
pred_gff will maintain it’s name in the match/match_part feature as the information is pulled directly from the input GFF3. But any pred_gff feature that becomes a final model will be renamed to something like “scaffold_1517-pred_gff_GeneMark.hmm-gene-0.6-mRNA-1” unless you specify map_forward=1 to maintain the original name.

—Carson



> On Jan 4, 2018, at 6:21 AM, Ole Kristian Tørresen <[hidden email]> wrote:
>
> Hi,
> as far as I can see, names or IDs of features in gffs given to pred_gff is included in the final output as the name of the feature. As far as I can understand, this is not expected behaviour (it is for model_gff). This is with MAKER 2.31.9.
>
> I have these settings:
> map_forward=0
> keep_preds=1
>
> I thought that map_forward had to be 1 to get the names for the old GFFs. Can you replicate this?
>
> Thank you.
>
> Sincerely,
> Ole K. Tørresen
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: Names/IDs from pred_gff are included in final gff

Ole Kristian Tørresen-2
Ok, but I have an entry in the final gff like this:
ID=maker-GmG20150304_scaffold_2371-pred_gff_maker-gene-0.125-mRNA-1;Parent=maker-GmG20150304_scaffold_2371-pred_gff_maker-gene-0.125;Name=ENSGMOT00000000668.1;_AED=0.00;_eAED=0.00;_QI=819|1|1|1|1|1|4|112|726;score=89.75616

(The name is derived from a pred_gff entry which is the results of mapping an old annotation to the new assembly).

This is then called ENSGMOT00000000668.1 protein AED:0.00 eAED:0.00 QI:819|1|1|1|1|1|4|112|726 in the proteins.fasta file. Which is unfortunate, because it apparently mapped 12 places in the assembly.

I have set map_forward=0, but keep_preds=1 (filtering on domain presence and AED score later).

This and another file (result of genemark_gtf2gff3), is not input as match/match_part to MAKER, but with gene/exon/CDS/mRNA. Could that be the issue?

Ole

 

> On 16 Jan 2018, at 19:15, Carson Holt <[hidden email]> wrote:
>
> pred_gff will maintain it’s name in the match/match_part feature as the information is pulled directly from the input GFF3. But any pred_gff feature that becomes a final model will be renamed to something like “scaffold_1517-pred_gff_GeneMark.hmm-gene-0.6-mRNA-1” unless you specify map_forward=1 to maintain the original name.
>
> —Carson
>
>
>
>> On Jan 4, 2018, at 6:21 AM, Ole Kristian Tørresen <[hidden email]> wrote:
>>
>> Hi,
>> as far as I can see, names or IDs of features in gffs given to pred_gff is included in the final output as the name of the feature. As far as I can understand, this is not expected behaviour (it is for model_gff). This is with MAKER 2.31.9.
>>
>> I have these settings:
>> map_forward=0
>> keep_preds=1
>>
>> I thought that map_forward had to be 1 to get the names for the old GFFs. Can you replicate this?
>>
>> Thank you.
>>
>> Sincerely,
>> Ole K. Tørresen
>>
>> _______________________________________________
>> maker-devel mailing list
>> [hidden email]
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>

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