QC Hi-C data

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2.3 years ago

gubrins ▴ 350

Heys!

I am new in working with Hi-C data and I was wondering how I could do a QC on it. I do not mean to know the sequencing parameters and so on, but to know if all my genome is well represented within this data. I aim to use Hi-C data for scaffolding a de novo genome and I need to know if the data is good. I've just found this software (https://github.com/cerebis/qc3C) but in the absence of a reference genome (as it is my case) you need to input the enzymes you used for digestion, and in my case the protocol is enzyme-free. Any suggestions? I would be extremely grateful!!

Thanks in advance!

QC Hi-C • 733 views

ADD COMMENT • link 2.3 years ago by gubrins ▴ 350

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How is it even possible to generate the fragments without digestion? Can you please share the reference protocol? For testing quality, I'd recommend mapping the reads to the draft assembly (as a single end by interleaving the fastq files).

ADD REPLY • link 2.3 years ago by Buffo ★ 2.4k

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thank for your reply! We are doing Hi-C and the library was produced with the Swift Bioscience kit

ADD REPLY • link 2.3 years ago by gubrins ▴ 350

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