IGC module annotated using eggNOG mapper v2
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Erwin Sentausa
Jun 24, 2020, 3:41:37 PM6/24/20
to NGLess
Hi all!
I'd like to use NGLess, hopefully to replace MOCAT2, especially for functional analysis of human gut microbiota. I saw that using the available igc module, the functional features available are not as complete as those of MOCAT2 as the annotation was made (I believe) using eggNOG mapper v1. I'm interested particularly in KEGG pathway and KEGG module, which are available in annotation using eggNOG mapper v2. So, I'd like to know if the igc module using the annotation of eggNOG mapper v2 is available.
Thanks in advance.
Cheers,
Erwin
Luis Pedro Coelho
Jul 13, 2020, 10:39:47 AM7/13/20
to Erwin Sentausa, NGLess List
Hi Erwin,
I'm very sorry for the delay in answering. We had a couple of coinciding deadlines at the end of June.
I have looked and we do not have an eggnog-mapper v2 annotation as part of the NGLess release.
We will in the not-so-distant future have a complete update of this, but, for the moment, we only have the published eggnog-mapper v1 annotations.
If you have the KEGG DB, you can go from KOs to Modules->Pathways (note too that pathways need to be analysed with a bit of care: there are a lot of false positives if you are not careful).
Best
Luis
Luis Pedro Coelho | Fudan University | http://luispedro.org
https://orcid.org/0000-0002-9280-7885
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I'm very sorry for the delay in answering. We had a couple of coinciding deadlines at the end of June.
I have looked and we do not have an eggnog-mapper v2 annotation as part of the NGLess release.
We will in the not-so-distant future have a complete update of this, but, for the moment, we only have the published eggnog-mapper v1 annotations.
If you have the KEGG DB, you can go from KOs to Modules->Pathways (note too that pathways need to be analysed with a bit of care: there are a lot of false positives if you are not careful).
Best
Luis
Luis Pedro Coelho | Fudan University | http://luispedro.org
https://orcid.org/0000-0002-9280-7885
> You received this message because you are subscribed to the Google Groups "NGLess" group.
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Erwin Sentausa
Jul 13, 2020, 11:32:38 AM7/13/20
to NGLess
Hi Luis,
Thanks for your reply. Finally I got the eggNOG mapper v2-annotated IGC database from a colleague. I replaced the annotation in the igc module with this and it seems to work well! But well, please do let us know when you have the updated version.
Thanks!
Erwin
On Monday, July 13, 2020 at 4:39:47 PM UTC+2, Luis Pedro Coelho wrote:
Hi Erwin,
I'm very sorry for the delay in answering. We had a couple of coinciding deadlines at the end of June.
I have looked and we do not have an eggnog-mapper v2 annotation as part of the NGLess release.
We will in the not-so-distant future have a complete update of this, but, for the moment, we only have the published eggnog-mapper v1 annotations.
If you have the KEGG DB, you can go from KOs to Modules->Pathways (note too that pathways need to be analysed with a bit of care: there are a lot of false positives if you are not careful).
Best
Luis
Luis Pedro Coelho | Fudan University | http://luispedro.org
https://orcid.org/0000-0002-9280-7885
On Wed, 24 Jun 2020, at 9:32 PM, Erwin Sentausa wrote:
> Hi all!
>
> I'd like to use NGLess, hopefully to replace MOCAT2, especially for functional analysis of human gut microbiota. I saw that using the available igc module, the functional features available are not as complete as those of MOCAT2 as the annotation was made (I believe) using eggNOG mapper v1. I'm interested particularly in KEGG pathway and KEGG module, which are available in annotation using eggNOG mapper v2. So, I'd like to know if the igc module using the annotation of eggNOG mapper v2 is available.
>
> Thanks in advance.
>
> Cheers,
> Erwin
>
> --
> You received this message because you are subscribed to the Google Groups "NGLess" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to ngl...@googlegroups.com.
quinten...@gmail.com
Nov 4, 2020, 9:43:32 AM11/4/20
to NGLess
Hi all,
Is there anything know about when the IGC database will be updated with the eggNOG mapper v2 annotations?
Would be nice to be able to use the updated IGC database =)
Best,
Quinten
Op maandag 13 juli 2020 om 17:32:38 UTC+2 schreef Erwin Sentausa:
Erwin Sentausa
Mar 1, 2021, 4:23:39 AM3/1/21
to NGLess
Hi Luis and everyone,
I wonder, does the IGC module in the latest release (1.3.0) already use the annotation using eggNOG mapper v2?
Thanks,
Erwin
Luis Pedro Coelho
Mar 1, 2021, 7:43:02 AM3/1/21
to Erwin Sentausa, NGLess List
The modules evolve somewhat separately from the main programme, so there has been no update to them in this release.
Best
luis
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