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xjtu-omics / HiCAT

HiCAT new project
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Monomer template #11

Open Jokendo-collab opened 2 months ago

Jokendo-collab commented 2 months ago

In situations where you do not have a monomer template, how do you run this kind of analysis? How confident is the result?

865699871 commented 2 months ago

Template sequence is used for StringDecomposer to split the satellite sequence. You need to make sure the species centromere sequence is satellite type. It's not suitable for other types, like TE-rich or point cen. If it is satellite type, you can try TRF and the pipeline we recent developed for building satellite library. It may help you to infer the centromere satellite. But the exact centromere sequence should be identified based on Chip-seq of CENH3.