Here's my data:
sample_A: Canonical assembly with gene models (sample_A.fasta, sample_A.gff3)
sample_B: Mutant and de-novo assembly. No gene models (sample_B.fasta)
I want to transfer the gene models from sample_A to sample_B.
I thought this would be straightforward but it's definitely not. There are some instances where exon_2 comes before exon_1 or where a particular exon maps multiple times on the de-novo assembly.
Is there a tool that will do this? Ideally, I would like a tool that does the following:
program --ref_assembly sample_A.fasta --ref_annotations sample_A.gff3 --query_assembly sample_B.fasta --percent_identity 0.98 > sample_B.gff3
Here is an example of a unique edge case when I've mapped the exons from transcript FUN_000463-T1(from sample_A.gff3 and sample_A.fasta) to the new assembly (sample_B.fasta). Notice the exon ordering:
Here's the left side zoomed in:
Here's the right side zoomed in:
Notice the exon ordering.