Allele table

[Rhia15]

Hi,

I am really keen to use this tool, however I am struggling with understanding and making the allele table. Please could I see what the gff3 format and .bed frmat should look like before using gmap2AlleleTableBED.pl as I keep getting the error: Use of uninitialized value $gene in pattern match (m//) at gmap2AlleleTableBED.pl line 21, <IN> line 1. Use of uninitialized value $gene in exists at gmap2AlleleTableBED.pl line 24, <IN> line 1.

If I understand correctly, you align your query genome with a reference genome ( a close diploid species?). And this is to define the allelic groups in your query genome... I don't quite understand how this alignment helps in identifying allelic groups, would there not be more allelic groups present in the query compared to the reference?

Does this also mean that I need a GFF file for both the query and the reference (diploid) genome to make the allelic table? So essentially, a good initial assembly? Can I use a scaffold level assembly and then annotate this through BRAKER to then get a GFF file?

Also, do you know how this would work in terms of centromeric repeat regions as it relies on the protein coding regions? (I think?)

Apologies for so many questions, I read the paper and a few issues concerning the allelic table but still did not seem to understand this.

Any help would be really appreciated.

Thank you, Rhianah