how to perform a RIP analysis using RIPCAL

Question

[huiyus97]

Hi,

I wanted to perform a RIP (Repeat-induced point mutation) analysis using RIPCAL on several fungal genomes, however, I am confused about how to perform this analysis.

Should I perform the RIP-index scan first to detect all RIP-mutated regions, and then extract all these regions into separate files? Then find an already been reported repeat family in the same fungal species which is free from RIP mutation, and use it as a reference to align each of my RIP-mutated regions to perform the alignment based RIPCAL analysis?

Thanks for your help!