Query about Micro-C data usage

[NMaziak]

Hello,
Thanks so much for this useful tool.

I had a quick question: I’m working with Micro-C data (paired-end, 150 bp reads), and I’m interested in mapping it in a way that preserves fragment-length information from the regions present in chimeric reads. My goal is to potentially analyze this similarly to MNase-seq.

Do you think minimap2 could be suitable for this? I was considering it as an option since it can align through large insertions, which might help avoid complications with supplementary alignments. Would you have any suggestions?

Would really appreciate your thoughts!

All the best,
Noura