[maker-devel] map2assembly

[Michael Thon]

Hi - 
We’re using map2assembly to map genes from other gene annotation pipelines onto the genome sequence in order to compare AED values to a maker de novo annotation.  We found a few transcripts that map2assembly maps to multiple loci in the genome.  Is there any way to know if these are all equally good alignments or are they all above some present threshold? I’m trying to decide what to do with the multiple mappings - whether we should discard all but one (in that case we’d need to decide which one) or whether we should keep them all.  Keeping them all makes the most sense but the problem is they all have the same id. should map2assembly append a number to the id when a transcript maps to multiple locations in the genome?