I have run RATT to transfer the annotation from a reference strain to another strain. For this, I have run:
$RATT_HOME/start.ratt.sh embl ref.fa output/annotation/ Strain
This creates several things in the working directory that I do not wish:
- a Sequences folder with the sequence in FASTA format of each chromosome
- a copy of the reference sequence in FASTA format (followed by a mysterious number)
- a copy of the query sequence in FASTA format followed by a mysterious number
I could not find any options in the RATT help to disable the creation of these files. Also, does anybody know why these files are created?