[Open-bio-l] Best practice for modelling data in GFF

[Dan Bolser]

Hi guys,

Not sure if this is the right forum, but I just thought I'd ask...

Where can I find information on 'best practices' for modelling
biological data in GFF?

For example, I'd like to model paired-end sequence alignments in GFF.
One suggestion was to use match/match_part to link each end into a
pair. Another option is to use 'read_pair' with 'contig' for the
parent feature...

Should I just be using SAM/BAM?

Seems a shame not to have a standard way to do this in GFF...


Cheers,
Dan.