Choose max size of gene flanking DNA parameter in gff2gbSmallDNA.pl script included in augustus

Question

[hsiaoyi0504]

Hi there:

I am trying to use augustus to do gene prediction, but the input file I have is in gff3 format. I am trying to convert gff3 files into genbank format using the script gff2gbSmallDNA.pl shipped with augustus. However, I don't know how to choose one of the parameter - max size of gene flanking DNA and it doesn't have a default value. Therefore, I somewhat get stuck. Can someone help me this? Thanks.

Answer 1

[h.mon]

Not exactly an informed answer, but I've seen 500 (SciLifeLab course), 1000 (Scipio tutorial and BUSCO sources) and 5000 (Augustus iterative training set tutorial).

I would go with 1000, it is a nice arbitrary number.