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motu-tool / mOTUs

motus - a tool for marker gene-based OTU (mOTU) profiling
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missing GTDB classification for motus_3 ids #97

Closed TianyiChang closed 1 year ago

TianyiChang commented 1 year ago

Hi there

Thanks for providing a GTDB annotation file. It seems that many motus were missing from 'mOTUs_3.0.0_GTDB_tax.tsv', such as the below:

meta_mOTU_v3_13058 meta_mOTU_v3_13316 meta_mOTU_v3_13553 meta_mOTU_v3_13666 meta_mOTU_v3_13677 meta_mOTU_v3_13799 meta_mOTU_v3_14519

I was wondering if there are quality issues associated with these missing motus?

Thanks!

AlessioMilanese commented 1 year ago

This meta-mOTUs have no genome or MAG, hence it was not possible to run GTDB-Tk.

I will fix the taxonomy next week (but basically for these there is no GTDB annotation).

TianyiChang commented 1 year ago

Thank you so much for your quick reply! It seems a bit strange since some of the query reads were assigned to these meta-mOTUs (there are 84 mOTUs in total in my case), which have no GTDB taxonomy information.

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​I look forward to hearing back from you.

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​Thanks again.

​

On Sep 23 2022, at 5:52 PM, Alessio Milanese @.***> wrote:

This meta-mOTUs have no genome or MAG, hence it was not possible to run GTDB-Tk.

I will fix the taxonomy next week (but basically for these there is no GTDB annotation).

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AlessioMilanese commented 1 year ago

The file it's updated now. We also added the GTDB annotation for each genome: https://zenodo.org/record/7146984#.Y0XdplJBwbk

TianyiChang commented 1 year ago

Thanks a lot!!

​

On Oct 11 2022, at 5:19 PM, Alessio Milanese @.***> wrote:

The file it's updated now. We also added the GTDB annotation for each genome: https://zenodo.org/record/7146984#.Y0XdplJBwbk

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