AGHGHGH PANAROO

[babayagaofficial]

it seems panaroo gives any duplicated gene a label DISTINCT from the duplicates in other places in the genome

which means that when we map panaroo's genes back to the genome it comes from, any genome with duplicates will have a bunch non-existent genes surrounding a real gene where there's duplication

so basically anything we've ever is wrong

therefore need to manually check for duplicates, somehow

[iqbal-lab]

Talk to Gerry, remember he's on our slack

[babayagaofficial]

have solution using the --merge-paralog flag in panaroo in b94dc9da820705651d305e633c199c687adf8596