How to specify -p and -t arguments in mob cluster without any information

[Abelcanc3rhack3r]

Hi, I managed to install the MOBsite via pip.

Now I have some other problem.

We have one fasta file containing 50 random plasmid sequences. Nothing else is known about plasmids.

We want to cluster the plasmid sequences. We use command mob_cluster, we put the fasta file as infile, but what do we put as the -p and the -t? it wont run without the two arguments.

Thanks

[kbessonov1984]

Hi,

The mob_cluster tool is used to update or build from scratch a plasmid database. There are some instructions on how to build and update database in this comment https://github.com/phac-nml/mob-suite/issues/20#issuecomment-476278194.

You can run mob_typer and see to which primary and secondary cluster(s) your 50 plasmid sequences will be assigned.

Provide more information on what you are trying to accomplish with a set of plasmids and what results are you getting from mob-typer.

[Abelcanc3rhack3r]

We are just trying to cluster the plasmids with each other, not necessarily with other known plasmids in a database

ok, I wil run the mob typer and share with you the results when we get them

[luciagrami]

Hello,

I have the same question. I run MOB typer on the new set of plasmids, but no sure how to create the taxonomy file, and also I couldn't find a sample file, so not sure how the taxonomy file looks like.

Thanks!

[jrober84]

I will update the documentation for MOB-cluster to improve it as there are few details available currently in the repo. But in the meantime, the taxonomy file is just a two column tab-delimeted file with the header id,organism. Where id is the sequence id of your plasmids you wish to add to your database and organism is the complete name that you want to associate with your sequence. The organism name must be present in the NCBI taxonomy for it to work correctly.

[luciagrami]

Thanks!