What is the expected sequencing output for a Hi-C library?

Question

[Panos]

I recently started playing with Hi-C data. The goal is to use them in order to scaffold a genome assembly. So I downloaded a single pair of files (_R1 and _R2) which contained >680 million reads! Does this sound familiar to anyone who has used Hi-C before? Is it usual to get so many reads when doing Hi-C sequencing?

I'm only asking because I'm more used to getting 50-70 million reads per (Illumina) run. Whenever I got more than that, it was because something went wrong during sequencing.

Answer 1

[ATpoint]

Yes, that is normal for these sorts of libraries, at least for human and mouse genomes. For data that are supposed to yield kilobase resolution one even has to sequence a billion or more reads, iirc that is what they did in this landmark paper from Lieberman-Aiden.