Maker annotation small DNA fragments

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Maker annotation small DNA fragments

Philippine De Boissel
Hello,

How are you?
I am new in bioinfo. I am working with circulating cell-free DNA (small DNA fragments with around 180 to 600 bp).

We sequenced a whole ccfDNA form a mussel, and I am trying to annotated those fragment (up to 100pb) with MAKER.

Is it a good idea?

I have been facing one problem...i am using clusters and I am not allow to have more than 1000k files. However, MAKER create sub-folders (maker_datastore) for each contigs. Is there a way to produce one big output during the process instead of many different files for each contigs, please?

Thank you very much

Philippine



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Re: Maker annotation small DNA fragments

Carson Holt-2
The fragments you are looking at are likely too small to annotate with MAKER. MAKER is more for assembly annotation. The gene predictors used will need a few hundred bp of lead in sequence before each gene to seed the HMM as well as complete intron/exon structure which you will not have in fragments that are only 180 to 600 bp. MAKER will create a separate work directory for each contig so that the programs MAKER calls can work independently on each without files colliding (that is how MAKER can scale to several hundred CPUs when ran in parallel via MPI for example).

—Carson


> On Aug 21, 2018, at 12:18 PM, Philippine De Boissel <[hidden email]> wrote:
>
> Hello,
>
> How are you?
> I am new in bioinfo. I am working with circulating cell-free DNA (small DNA fragments with around 180 to 600 bp).
>
> We sequenced a whole ccfDNA form a mussel, and I am trying to annotated those fragment (up to 100pb) with MAKER.
>
> Is it a good idea?
>
> I have been facing one problem...i am using clusters and I am not allow to have more than 1000k files. However, MAKER create sub-folders (maker_datastore) for each contigs. Is there a way to produce one big output during the process instead of many different files for each contigs, please?
>
> Thank you very much
>
> Philippine
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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