missing CDSs in gene_presence_absence.csv?

[memoriasresiduais]

Hi,

I have CDSs in the gff files that are absent in the gene_presence_absence.csv file... Shouldn't all be there?
I don't understand why these are ignored or excluded... I'm using version 3.6.0.
Any thoughts and help will be welcome.
Thanks in advance!
Alexandra

[andrewjpage]

Hi,
As a first step could you update to the latest version (3.11.0).
Some things get filtered, like very small CDS's etc...
Andrew

[memoriasresiduais]

Thanks for the quick feedback, Andrew. Some of them are large CDS, so it's kind of strange...
I'll update the version and let you know if the problem is solved. Thanks!
Best,
Alexandra

[andrewjpage]

If they are large CDS's you should also check that they arent pseudogenes.

[andrewjpage]

From version 3.12.0 the minimum gene size has been dropped to 18 nucleotides from 120.

[memoriasresiduais]

Thanks for the info, Andrew, and for all the beautiful tools you’ve been developing and sharing with the community! Have a nice day! De : andrewjpage [mailto:notifications@github.com] Envoyé : mercredi 31 janvier 2018 11:05 À : sanger-pathogens/Roary <Roary@noreply.github.com> Cc : Alexandra Moura <amoura@ua.pt>; Author <author@noreply.github.com> Objet : Re: [sanger-pathogens/Roary] missing CDSs in gene_presence_absence.csv? (#367) From version 3.12.0 the minimum gene size has been dropped to 18 nucleotides from 120. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#367 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AZOwRb2tXmzmFTXqbKQL4jFUIGaSfmFdks5tQDq8gaJpZM4Q3t-C>.

[Amilycd]

Hi, I encountered the same problem as you. Have you solved it? If so, what method did you use?

[memoriasresiduais]

Hi there,
I think the new version at the time solved the problem, but as I also found other problems in the grouping of gene families (i.e. identical proteins being split into different groups and different proteins within the same one - see #616), I switched to PanACoTA...