[maker-devel] creating fasta ids

[Craig Coleman]

Hi,
I have a fungal genome that I successfully ran through Maker.  Rather than running GeneMark directly in Maker I ran it separately and generated a gff file.  I provided this gff file to Maker and ran SNAP and Augustus as well.  The GeneMark gff3 file contained unique IDs for genes that are carried over into the protein and transcript fasta files.  These IDs are included in the Maker gff file as the name given for the mRNA feature but Maker creates a different ID for the GeneMark generated features in the gff file.  When I run maker_map_ids to create a mapping file of gene and transcript IDs, the program uses the Maker generated ID instead of the GeneMark generated name.  Then when I run map_fasta_ids the Maker IDs in the map file do not match the names of the GeneMark proteins and transcripts in the fasta file.  Protein and transcript models generated by SNAP and Augustus map just fine.  I am hoping someone has a suggestion on how to solve this problem.

Craig Coleman

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