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Post Processing of Annotations

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Post Processing of Annotations

nathan.ricks
Hi,
I've been running your Maker pipeline, and I've reached Post Processing of Annotations portion. In your Online training you use the output.blastp and the outuput.iprscan files to help assign function.
My question is what format do these files need to be in.
Iprscan can produce files in a variety of formats: tsv, xml, gff3, html and SVG
while blastp can produce the tabular, pairise, xml and a number of others.

Thanks

Nathan Ricks

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Re: Post Processing of Annotations

Carson Holt-2
Use blastp with the the tab delimited format option and the UniProt/Swiss-Prot database. What additional filters you choose to set (i.e. e-value limit) may vary, although I would recommend 1e-6 or lower.

—Carson

> On May 3, 2017, at 10:19 AM, Nathan Ricks <[hidden email]> wrote:
>
> Hi,
> I've been running your Maker pipeline, and I've reached Post Processing of Annotations portion. In your Online training you use the output.blastp and the outuput.iprscan files to help assign function.
> My question is what format do these files need to be in.
> Iprscan can produce files in a variety of formats: tsv, xml, gff3, html and SVG
> while blastp can produce the tabular, pairise, xml and a number of others.
>
> Thanks
>
> Nathan Ricks
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: Post Processing of Annotations

Ence,daniel
In reply to this post by nathan.ricks
Hi, The iprscan output should be in tsv format, which is tab-separated, and the usage statement for the maker_functional_gff says that the blastp output should be in “wu-blast -mformat 2”, which I think is tabbed too.

~Daniel

 

> On May 3, 2017, at 12:19 PM, Nathan Ricks <[hidden email]> wrote:
>
> Hi,
> I've been running your Maker pipeline, and I've reached Post Processing of Annotations portion. In your Online training you use the output.blastp and the outuput.iprscan files to help assign function.
> My question is what format do these files need to be in.
> Iprscan can produce files in a variety of formats: tsv, xml, gff3, html and SVG
> while blastp can produce the tabular, pairise, xml and a number of others.
>
> Thanks
>
> Nathan Ricks
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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Re: Post Processing of Annotations

Carson Holt-2
In reply to this post by Carson Holt-2
The maker_functional_gff and maker_functional_fasta scripts pull specific fields out of the UniProt fasta header, so they are tied to the format used by UniProt/Swiss-Prot. At one time I had modified them to also work with NR, but that was several years ago, so I don’t know if it would still work.

—Carson



On May 3, 2017, at 1:10 PM, Nathan Ricks <[hidden email]> wrote:

Is it possible to make my own database from sequences that I have downloaded form NCBI instead of using the UniProt/Swiss-Prot?

On Wed, May 3, 2017 at 10:30 AM, Carson Holt <[hidden email]> wrote:
Use blastp with the the tab delimited format option and the UniProt/Swiss-Prot database. What additional filters you choose to set (i.e. e-value limit) may vary, although I would recommend 1e-6 or lower.

—Carson

> On May 3, 2017, at 10:19 AM, Nathan Ricks <[hidden email]> wrote:
>
> Hi,
> I've been running your Maker pipeline, and I've reached Post Processing of Annotations portion. In your Online training you use the output.blastp and the outuput.iprscan files to help assign function.
> My question is what format do these files need to be in.
> Iprscan can produce files in a variety of formats: tsv, xml, gff3, html and SVG
> while blastp can produce the tabular, pairise, xml and a number of others.
>
> Thanks
>
> Nathan Ricks
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org




_______________________________________________
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[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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