How can I Extract Transposable element from a new genome assembly?

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Hello All,

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.


genome


transposons


assembly


annotations

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