EI-CoreBioinformatics / mikado

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.
https://mikado.readthedocs.io/en/stable/
GNU Lesser General Public License v3.0
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missing explaination of mikado.bed in tutorial #385

Closed cooketho closed 3 years ago

cooketho commented 3 years ago

Can you please help me understand something about the tutorial? I'm reading here:

https://mikado.readthedocs.io/en/latest/Tutorial/

and I see at the mikado serialize step there is a command which uses a file called mikado.bed:

mikado serialise --json-conf configuration.yaml --xml mikado.blast.xml.gz --orfs mikado.bed --blast_targets

but I can't seem to find any step where this file was created, or any previous reference to it in the tutorial. I see a reference to orfs.bed, which the tutorial indicates is from transdecoder. Is this a typo, and the command should have passed orfs.bed to --orfs? Or is this something else? Furthermore, it looks like the text of that command got cut off in the tutorial because --blast_targets needs an argument, but it doesn't have one.

Thanks!

lucventurini commented 3 years ago

Dear @cooketho

Thank you for pointing this out! We are reviewing the documentation these days and we'll make sure to explain this better.

Next Monday I will try to clarify it here as well.

Many thanks again for using our tool and for coming to us with this question, it helps us making Mikado ever better.

Kind regards

Luca Venturini

lucventurini commented 3 years ago

Dear @cooketho

Many apologies for the delay, we were swooped up by our quest to improve the code coverage for the suite.

I have update the documentation (see 8b63828) and we will bring it up live soon.

Kind regards,