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lobbytruckers 01-23-2017 10:10 AM

Minimum sequencing (and coverage) requirement for human ATAC-seq libraries?
Hi all,

I just got some multiplexed ATAC-seq libraries done, where I got anywhere between 50-90 million reads per sample. Greenleaf's current protocol article ( suggests that anywhere > 50 mil mapped reads is good to infer open chromatin in human samples, whereas you need > 200 mil reads to footprint transcription factors. We usually do paired end HiSeq 3000 runs.

Can anyone who has done ATAC-seq on human genome provide some insight? What raw read numbers were you shooting for? What kind of coverage is acceptable for publication? How many HiSeq or NextSeq lanes/cells did you end up using?

I'm trying to figure out how much more sequencing we need to do in order to get results that are publishable based on the norms (mostly for coverage) but I'm not too familiar with a lot of ATAC-seq publications yet (besides the primary Greenleaf publications), so if anyone else has an input on this, I would really appreciate it! With the above mentioned metrics, I'm currently at ~3x average coverage for the entire human genome.
Thanks so much!

vadoue 09-01-2017 05:56 AM

Hi you!

I was wondering if you got your answer. Also I saw that you used HiSeq3000. Did you used 2x75 or 2x150bp reads? I am planning to use 2x150 and I was wondering if I could "lost" small fragments information...

Thank you! :)

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