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.
1 answer
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.
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