I have a bed file containing annotations for transposable elements that were generated from an old genome assembly. However, I have a new assembly which I believe to be superior and would like to use the old annotations to obtain TE coordinates from the new assembly.
What I tried>
Obtain fasta sequence from old genome. mapp this with bowtie2 to new genome to get aligned reads (--al).
The issue here is that, the new fasta generated contained the old contig names instead of the new contig names in the new genome.
Is there a different way to go about this to arrive at my goal without beginning annotation with repeatmasker from scratch?
I tried to use repeatmasker earlier but the output didnt look right to me and I'd rather just fetch the TEs from the new genome.
Thanks in advance.