Is it possible to run panaroo_2_pagoo without removing "refound_"?

[emilywollmuth]

I am working with a divergent group of organisms, so I want to keep the genes refound by panaroo because I believe the core genome is being underestimated without them. My understanding is that the genes labeled "refound_" are not inherently a problem. Instead, it's the genes with the "stop" marker that are likely pseudogenes. Is there a way to run panaroo_2_pagoo and not remove all "refound" genes but to still remove "_stop" genes?

Alternatively, is it possible to use panaroo_2_pagoo and remove no genes or to make a pagoo matrix directly from a csv matrix instead of the long format data? If this isn't possible, I'll just need to convert the panaroo matrix to long format for pagoo to reformat it back into a matrix again.

Thanks for your work on this package. Pagoo is great and so easy to use!

[iferres]

Hi @emilywollmuth , currently the only way is to manually create a Pagoo object using the long format ( https://iferres.github.io/pagoo/articles/Input.html ) including those marked genes. I should probably consider to modify this function to include them, but I don't have the time to do it right now. Sorry :(

I wrote this function some time ago, so I'm not sure, but I think it was a problem when reading the csv AND the gffs because the "_refound" "_stop", etc, genes were not present in the gff files so Pagoo couldn't match ids with their sequences. For sake of simplicity I decided to remove them all, but you're right that ideally they shouldn't be a problem when working only with the csv file.

I'll leave the issue open but sincerely I don't know when will I address it.

[emilywollmuth]

Thanks for the quick response @iferres! No worries. I figured it was because the gff matching issue that would arise that the program doesn't do this. I'll manually create a Pagoo object.