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We are new to ATAC-Seq. We have performed library validation and several of our samples have produced results similar to those in the image attached. We have a single large peak at 186 bp. Are we okay to go ahead for sequencing? Thanks a lot.
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I forgot to mention that above samples are from FACS mouse cells. We also tried IP instead of FACS, which gave us multiple small peaks, which method shall I go on? Any suggestion is greatly appreciated. -
We run qc chips for people doing ATACseq with some frequency. I'm never sure what a "good" result is.
I guess you want a large percentage of your DNA to be in the nucleosome monomer size range? But you also want to see some multimers? Not sure.
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PhillipComment
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It seems that your library is over tagmented. Maybe you should decrease the incubation time while performing the tagmentation.Comment
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I would also say that it is over-tagmented. Which Tn5 are you using, Nextera or home-made? Maybe there is too much Tn5 for the number of cells you are using?Comment
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Here is what my ATAC libraries look like. I agree that optimization of tagmentation enzyme amount or time should be considered.
What is you input amount? Are you starting with <50,000 cells? Smaller input amounts will require less enzyme and/or shorter incubation.Last edited by RickC7; 06-14-2018, 08:25 AM.Comment
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same profile
Did you solve this? My libraries look like yoursComment
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Does my library look ok?
Hello, I performed ATACseq preparation of librarys I used 50.000 cells counted by en bauer chamber, and following the protocol of Buen rostro, I did 25 cycles in total of PCR. Can someone tell me if this library looks ok? (attached pdf 1st sample) I am not sure about it. Thank you so much for your help
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CamilaComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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