repeatmasker output gff

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repeatmasker output gff

Homa Papoli
Hello,

I have 2 questions regarding user maker:

I have used repeatmasker for my genome separately and I have a gff file. However, my gff file, in the third column, has the word "similarity". In a workshop I had taken on genome annotation, it was said that the gff for maker should have "match" and "match_part" for the third column. I was wondering whether I could use the original gff output of repeatmasker or should I make any changes to it?

Another question is about running maker. Since maker takes several days to run, if the job gets interrupted due to limit in days of running the job, I was wondering whether it is possible to re-start maker from where it got interrupted?

Thank you,
Homa

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Re: repeatmasker output gff

Carson Holt-2
It needs to be a two level feature. match/match_part is one example, others will work as long as when it is assembled it is two levels.

MAKER saves it’s state as it runs, so you can restart it at any time without losing progress.

—Carson


> On Mar 25, 2020, at 2:38 PM, Homa Papoli <[hidden email]> wrote:
>
> Hello,
>
> I have 2 questions regarding user maker:
>
> I have used repeatmasker for my genome separately and I have a gff file. However, my gff file, in the third column, has the word "similarity". In a workshop I had taken on genome annotation, it was said that the gff for maker should have "match" and "match_part" for the third column. I was wondering whether I could use the original gff output of repeatmasker or should I make any changes to it?
>
> Another question is about running maker. Since maker takes several days to run, if the job gets interrupted due to limit in days of running the job, I was wondering whether it is possible to re-start maker from where it got interrupted?
>
> Thank you,
> Homa
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


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