--remove-invalid-genes output

[oeco28]

Hello,
I have a practical question. After looking at the output of panaroo with the option to remove invalid genes, IT has come to our attention that there are gene annotations in the matrix that do not correspond to any gene in the input gffs. The annotations are in the form of #refound##_stop. What is the best practice to deal with these cases? Remove them from the analysis?
Our inclination is to conservatively remove the annotation . Any recommendation is appreciated

regards
Omar

[gtonkinhill]

Hi,

Panaroo will attempt to find genes that have been missed in the initial annotation of each genome. These are labelled as 'refound'.

Genes with premature stop codons or of unusual length are also labelled with '_stop' or '_len' respectively. Depending on your use case you might want to filter these out. These annotation can be filtered from the presence/absence matrix using the panaroo-filter-pa script.

I hope this helps!

[oeco28]

Yes!
I had only seen the #_refound#_stop. My feeling was also to filter them out and I had written s script to remove those (fill with NA). But I wanted to make sure that this is the "best practices"
thank you