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salvadorlab / mbovpan

Mbovpan is a nextflow bioinformatic pipeline for Mycobacterium bovis pangenome analysis. The goal of Mbovpan is to help researchers to study the M. bovis pangenome in an automatic and easy way.
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Core phylogeny + hypothetical protein naming using BLAST #26

Closed noahaus closed 7 months ago

noahaus commented 7 months ago

Would be useful to take the core genome phylogeny and annotate the edges with M. bovis genes that are considered virulent for for the species.

Step 1) BLAST the pangenome_reference file against the M. bovis genome. Only have unique lines in the output Step 2) Change the original names to their pseudogene result Step 3) Filter by matching in the mbovis virulent list Step 4) plot the accessory genes that pass the filter alongside the core genome phylogeny.

noahaus commented 7 months ago

Step 1 - easy peasy Step 2 - done step 3 - not necessary if we tie the output to specifically what is in the M. bovis genome

noahaus commented 7 months ago

Output figure for these genes

image

Will just do some midpoint rooting, and it will be nice to have a way to summarize the node support - but on the right direction

noahaus commented 7 months ago

Midpoint done - and I'm thinking that with that, we can divide the work based on the outputs. mbovpan should be useful to generating outputs, making the figures and tables that I am interested in should be the responsibility of the researcher.