Adapt processing shotgun metagenomes

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Rémy Dugauquier

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Aug 17, 2020, 7:19:22 AM8/17/20
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Hello,

I would like to make functional profile of some genes by using the OMRGC.v2 instead of OMRGC.v1 with the pipeline marine-profiler.ngl. Do you have an idea how I could do this?

Thank you for your help,

Have a nice day,

Dugauquier Rémy

Luis Pedro Coelho

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Aug 21, 2020, 8:12:32 AM8/21/20
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Dear Rémy,

Sorry for the slow response, but it's holiday time...

You'd need two pieces of data:

1. The actual FASTA file

2. An annotation file for each gene (these can be generated with eggnog-mapper and recent versions of NGLess can just consume the output of eggnog-mapper without further processing).

I am not sure we (or the Bork group, @Renato, do you know?) have an up-to-date version of #2 (in particular, for eggnog-mapper2).

Best
Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org
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Renato Alves

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Aug 21, 2020, 9:55:58 AM8/21/20
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Hash: SHA256

We seem to have only eggNOG 4.5 annotations (from 2017).
I'll launch the job over the weekend and. Should be available sometime next week.

Cheers,
Renato

On 8/21/20 2:12 PM, Luis Pedro Coelho wrote:
> Dear Rémy,
>
> Sorry for the slow response, but it's holiday time...
>
> You'd need two pieces of data:
>
> 1. The actual FASTA file
>
> 2. An annotation file for each gene (these can be generated with eggnog-mapper and recent versions of NGLess can just consume the output of eggnog-mapper without further processing).
>
> I am not sure we (or the Bork group, @Renato, do you know?) have an up-to-date version of #2 (in particular, for eggnog-mapper2).
>
> Best
> Luis
>
> Luis Pedro Coelho | Fudan University | http://luispedro.org
> https://orcid.org/0000-0002-9280-7885
>
>
> On Mon, 17 Aug 2020, at 1:19 PM, Rémy Dugauquier wrote:
>>
>> Hello,
>>
>> I would like to make functional profile of some genes by using the OMRGC.v2 instead of OMRGC.v1 with the pipeline marine-profiler.ngl. Do you have an idea how I could do this?
>>
>> Thank you for your help,
>>
>> Have a nice day,
>>
>> Dugauquier Rémy
>>
>>
>> --
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>
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- --
Renato Alves, Dr. rer. nat.
EMBL Bio-IT & HD-HuB (de.NBI, ELIXIR Germany), Heidelberg, Germany

Email: renato...@embl.de
Github/Gitlab: @unode - Twitter: @renato_alvs
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Luis Pedro Coelho

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Sep 2, 2020, 4:51:39 PM9/2/20
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Hello Rémi (and others),

Renato uploaded the annotations to zenodo

We will wrap them into an NGLess module, but you can also already use them if you download them and run them with

...
counts = count(mapped,
map_file="prok-OM-RGC-v2.0.0.emapper.annotations-v2.tsv.xz")
...

The FASTA file for prok-OM-RGC-v2 is also available: https://www.ocean-microbiome.org/

HTH
Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org
https://orcid.org/0000-0002-9280-7885

> an email to ngless+un...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/ngless/4e0b77f3-812f-c628-07be-aa3d10c7050f%40embl.de.
>

Rémy Dugauquier

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Feb 9, 2021, 3:43:17 AM2/9/21
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Dear all,

First of all my apologies for the delay in responding. I had to put this work aside from my project for a while. But now I am starting to use NGLess again. A big thank you for your answers. I did an NGLess test with my data with the OMRGCV1 suggested in your tutorial and everything works fine. I now want to use it with the OMRGCV2. So if I want to use OMRGCV2 in a script, I have to upload the annotation to zenodo, but I don't see how to include that in an .ngl script to use it with my data. Could you tell me what to include in my .ngl script?

Thanks for your help,

Regards,

Dugauquier Rémy


ullo...@googlemail.com

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Feb 9, 2021, 1:09:33 PM2/9/21
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I would guess
counts = count(mapped,
map_file="prok-OM-RGC-v2.0.0.emapper.annotations-v2.tsv.xz")
as Luis suggested?
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