Hi there,
I'm looking to be able to directly align/compare/relate two versions of the human genome. Essentially, I have two pairs of fasta/GTF files: one is a known version of the human genome (the PRI assembly from gencode) and the other is a fasta file from an unknown version and a custom GTF of human endogenous retroviral sequences. My goal is to be able to relate the HERV sequence locations to nearby genes in the human genome found in the first GTF I mentioned.
So, in one GTF, it says "this HERV is at position X in this corresponding fasta file." In the other, it says "this gene is at position Y in GRCh38." How can I relate these? Is there a tool to "update" a GTF to a new assembly? Or to align two entire fasta files and view their relations to separate GTFs, something akin to custom UCSC genome browser?
I have the ability to code a solution from the ground up, but I want to ask if there is anything that may help before I spend a day or two doing it. Does anyone have any ideas? I'm open to them.
