Dorado repeat expansion

[tanyasarkjain]

This is a general question.
I used nanopore for some sequencing of a repeat expansion, I'm finding no reads in the repeat expansion - only flanking the expansion, after base calling with the sup model. Is there some other processing I need to do in order to view the repeat expansion reads? Thanks!

[Psy-Fer]

Hey,

I'm not from ONT but I'm working on repeats.
How long is the repeat you are looking at?
How did you align?
If it's a really long repeat and you didn't get any fully spanning reads, then try looking at soft clipped ends of reads going into the repeat.

Does the repeat have any similarities with any other repeat in the genome?

James

[tanyasarkjain]

I just used dorado aligner, but even looking at the reads from the base calling step using base caller I'm not seeing any reads in my region of interest. I