refMG versus mOTU

[mette Joergensen]

What is the relationshjp/difference between using refMG and mOTU ? 

Is the same marker that are used with the two methods ?

In the ng-metaprofiler why do you first map to refMG and only map the mapping reads to mOTUs ?

Best,

Mette

[Luis Pedro Coelho]

Dear Mette,

The answer has actually changed now that motus 2 (including 2.5) is available (it wasn't when the ng-metaprofiler paper was published).

It used to be to mimick how the original MOCAT-based motus worked (https://sunagawalab.ethz.ch/motu-tool/tutorial.motu.html), but we now should just recommend that people use motus 2+

I created an issue for this: https://github.com/ngless-toolkit/ng-meta-profiler/issues/2 I just want to run a test before actually pulling the trigger, but it should be very easy to switch.

Best

Luis

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

https://orcid.org/0000-0002-9280-7885

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[mette Joergensen]

Dear Luis

Do you have an idea about when mOTUs version 2.5 will be available ? I got the following error when trying to import the module. 

Could not connect to https://ngless.embl.de/resources/Modules/motus.ngm/2.5.tar.gz 
Best,

Mette

[Luis Pedro Coelho]

Hi Mette,

This should be an FAQ by now, but the truth is that we didn't do a very good job in this API.

The motus 2.5 profiler is not a part of the core NGLess like the mOTUs v1 was. Rather, it is an "external module" (we didn't have external modules when we added the motus v1).

Hopefully the instructions here make sense:

https://github.com/ngless-toolkit/ngless-contrib/tree/master/motus.ngm

HTH

Luis

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

https://orcid.org/0000-0002-9280-7885

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[mette Joergensen]

Thanks Luis

I also realised that it was an internal module just before reading your reply. I have now downloaded the 2.5 directory from https://github.com/ngless-toolkit/ngless-contrib/tree/master/motus.ngm into my Modules/motus.ngm directory. Is that the correct way to do it ? When I run my script I just get an erroe that I'm using the wrong python version but that is an error meassage that is understandable.

Best,

Mette

[Luis Pedro Coelho]

Thanks Luis

I also realised that it was an internal module just before reading your reply. I have now downloaded the 2.5 directory from https://github.com/ngless-toolkit/ngless-contrib/tree/master/motus.ngm into my Modules/motus.ngm directory. Is that the correct way to do it ?

Yes, that is correct.

When I run my script I just get an erroe that I'm using the wrong python version but that is an error meassage that is understandable.

That is progress of some sort :)

Luis

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