I need to create a kind of "translation file" between two versions of the same genome. The two genomes use a completely different naming system. I would like to know what ID on genomeA corresponds to what ID on genomeB.
Is there an easy way or a tool for this?
I thought about two strategies but none really convinced me:
1- Blast genes from versionA to the versionB genome, keep the best hits, use a script to extract the genes matching each position from annotationB, considering a kind of sliding window since the stast-stop position of the blast hit, may not exactly correspond to the start position of a gene on the annotationB (pretty hard considering my coding skills).
2- Trying to align sequences of geneA on indexed genomeB with Bowtie (got errors, since I'm not working with reads).
Thank you very much