Jon Palmer
Jon Palmer
The pipeline is setup in `funannotate train` to pass multiple pairs of Illumina files which get cleaned up and passed to Trinity. If you let funannotate run Trinity all the...
Most of the time these errors are related to gene identifiers (ID=) that are parsed incorrectly. The pipeline is setup to use NCBI like locus_tags, ie VC83_000001 or FUN_000001 --...
The ENV variable FUNANNOTATE_DB is not set so it can't find the file used to convert the go ontology annotations.
Hi @drabe004. Sorry to hear you are getting in trouble on your cluster! The most genomes I've ever run through `compare` is probably like 12. The script was really written...
Hi @drabe004 . What do you mean by "NCBI formatted files for CDS"?
Genbank (NCBI) format is highly problematic for alternative transcripts -- there is actually nothing in the format to link an mRNA features to a CDS feature. but that isn't really...
Oh, yeah you are right... However, I'd caution against ever using common names and not locus_tags as its a recipe for disaster. locus_tags are unique while common names inferred by...
It's reasonable to add more information to the FASTA header, I'll likely implement this in GFFtk as that is what the "new" funannotate2 uses in the backend.
Augustus v3.5 is not compatible with the version of funannotate you are running, downgrade Augustus.
You have an old version of funannotate, try upgrading to latest in master with pip.