I have a quick followup question about minus strand genes:

Here is a line of data:

scaffold3201|size9483    AUGUSTUS    transcript    9115    0    0.86    -    .    ID=g68389.t1;Parent=g68389

According to this, the feature begins at base 9115 and ends at base 0. However, GFF is one-based. The start and end positions of a feature are supposed to be positive integers. However, this transcript is transcribed from the minus strand, and so the coordinate system may be different.

By contrast, BED format uses interbase coordinates, where end is always greater than start, no matter if the gene is on the plus or minus strand.

Interbase (and bed files) define blocks, or ranges, of genomic sequence using start and end coordinate pairs (s,e) where s (start) indicates the index of the first base and e (end) indicates the index of the first base not included in the range. In addition, e >= s and the length of a range (the number of bases it covers) is always e - s.

See: http://transvar.org/6111/interbase.pdf

(This is from a class I taught on bioinformatics programming many years ago :-)

I want to convert this line of data to BED format. What should be the correct coordinates for start and end in BED?

Sorry, I just realized Augustus GFF does not report exons - just CDSs.