Katharina Hoff
A user informed us that WebAUGUSTUS currently rejects his hints file wiht source=M hints. The file looks like this: ``` CTG93 EVMpout start 124803 124805 0 - 0 source=M CTG93...
I have an Ubuntu 20.04 and followed the package install instructions at https://github.com/Gaius-Augustus/Augustus/blob/master/docs/INSTALL.md#HTSlib bam2wig fails to compile. (Not a problem for me personally, but probably annoying for other users) Message:...
A user reported by email: Hello, I have an error when I use Augustus, I run the code as: augustus --species=verticillium_albo_atrum1 --AUGUSTUS_CONFIG_PATH=/public/home/software/opt/bio/software/augustus/3.3.3/config/ --uniqueGeneId=true ../../repeat2/V991.rawchrom.FINAL.fasta.masked >V991-rep2.gff But the V991-rep2.gff file generated...
Code from issue https://github.com/Gaius-Augustus/BRAKER/issues/368 by Tomas should be updated from master
We need to find someone to implement this.
It is currently not possible to switch genetic code table for running BRAKER. AUGUSTUS can use a different genetic code, but GeneMark-ES/ET must be extended before BRAKER can be extended....
Extend BRAKER to separate stranded RNA-Seq, probably with samtools like this: https://www.biostars.org/p/92935/ Use counts of putative splice sites to find correct strandedness of data. Treatment of stranded RNA-Seq is important...
Replace aa2nonred.pl (which selects randomly one of several highly similar training genes) by a method that identifies rendundancy and then selects the best isoform consistently. This is in GALBA now...