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xjtu-omics / HiCAT

HiCAT new project
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HiCAT takes a monomer template and a centromere DNA sequence as inputs #7

Closed ZhouTaoWang closed 1 year ago

ZhouTaoWang commented 1 year ago

How to get monomer template and a centromere DNA sequence? Thank you!

865699871 commented 1 year ago

You can find the answer in our previous reply. #4 Determine centromere sequence need a systematic work. Functional centromere is determined based on CENH3 chip-seq. The centromere sequence of most animals and plants are huge tandem repeat, so you can try TRF. This review may help you know more about centromere (PMID: 32035948).

colindaven commented 10 months ago

I have also been trying to find centromeres in various plant genomes.

Practically, I found running Centrominer from https://github.com/aaranyue/quarTeT to be very good. Sometimes it can find centromeres automatically.

However sometimes Centrominer fails (basically picks telomeres as centromeres), but you can still take the TRF repeats in GFF3 format from the directory TRgff, catthem together, and manually select a better centromere candidate using the gff3in the tool JBrowsefor example. You can use peaks from the browser TRF track to estimate centromere location.