Alignment with new reference

Question

[marco.barr]

Hello everyone, I'm seeking advice from you regarding aligning to a reference. I've analyzed my ONT sequences, generated using a Ligation Sequencing Kit, with the dorado tool against the hg38 reference. In data analysis, I've noticed a coverage drop at the enzyme cleavage site, resulting in a subsequent reduction in the signal of the modified bases I'm calling. I'd like to realign my sequences to a reference that doesn't include the base segment corresponding to the enzyme interval. How can I achieve this? Do I need to modify hg38 or what's the approach? Thank you very much for your advice.

[GenoMax]

I'd like to realign my sequences to a reference that doesn't include the base segment corresponding to the enzyme interval. How can I achieve this? Do I need to modify hg38 or what's the approach?

Not completely clear why you want to do this (aligner should identify a deletion if it exists) but if you wish to exclude a part of the reference you could replace that sequence with N's. If you simply delete the part then it will throw the coordinates/reading frame out of order.