Question: Choose max size of gene flanking DNA parameter in gff2gbSmallDNA.pl script included in augustus
1
gravatar for hsiaoyi0504
12 months ago by
hsiaoyi050440
Taiwan
hsiaoyi050440 wrote:

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.

augustus • 383 views
ADD COMMENTlink modified 12 months ago by h.mon24k • written 12 months ago by hsiaoyi050440
1
gravatar for h.mon
12 months ago by
h.mon24k
Brazil
h.mon24k wrote:

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.

ADD COMMENTlink written 12 months ago by h.mon24k
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