You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
right now, the fromfile format doesn't support a simple way to produce translated sequence - presumably we'd need to add a CDS column or something, or else build workflows (elsewhere) to do prodigal-style coding sequence extraction, although that would only work for bacteria and archaea, so a CDS column might still be necessary.
I find myself using fromfile for everything these days, because it makes naming sketches properly so easy!!
So I would like us to support translate if we can -- perhaps as an additional param, e.g. -p k=10,k=7,scaled=200,protein,translate? Note it needs to have both of these, because we could alternatively translate into dayhoff.
I see your point about eukaryotes -- I would be happy to use a cds_filename column for this functionality.
current use case: a bunch of MAGs. Yes, I'll run prodigal-style translate separately, but for reasons I also want to build some 6-frame signatures
right now, the
fromfile
format doesn't support a simple way to produce translated sequence - presumably we'd need to add a CDS column or something, or else build workflows (elsewhere) to do prodigal-style coding sequence extraction, although that would only work for bacteria and archaea, so a CDS column might still be necessary.See @bluegenes comment too.
The text was updated successfully, but these errors were encountered: