search

zstephens / telogator2

A method for measuring allele-specific TL and characterizing telomere variant repeat (TVR) sequences from long reads.
MIT License
11 stars 1 forks source link

Running telogator using zebrafish genome #4

Closed Jokendo-collab closed 2 weeks ago

Jokendo-collab commented 1 month ago

I find this tools interesting and I would like to use it in my zebrafish assembly. How can I generate a telogator.fa for my zebrafish data? I see it is loading human telogator.fa and this could not work well with my data. I look forward to your advise on how to do this.

zstephens commented 1 month ago

Greetings! I just added a make_telogator_ref.py script to the repository, which should allow you to make a subtelomere reference that Telogator2 can accept via the -t input option. Example usage:

python make_telogator_ref.py -i input-ref.fa -o output-telogator-ref.fa -s zebrafish

Note that if zebrafish has different telomere repeats (or variant repeats) than human, you might need to make an alternate kmers.tsv file.

zstephens commented 2 weeks ago

Closing this for now, feel free to reopen if you have additional questions.