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Hi all,
I have recently prepared a pool of 9 ATAC-seq libraries from mouse hearts and performed a MiSeq Nano run to validate my pooling calculations, as it's difficult to accurately quantify the libraries.
From the data I’ve received (~1 million 150bp PE reads), it looks like most of the samples were pooled correctly (in terms of read number yield).
The alignment rates (~75-80% of uniquely mapping reads, ~15% mapping more than once) and mitochondrial contamination (less than 5%) seem fine to me as well.
What I was wondering is whether there is any other information that I can extract out of this run to be confident in my ATAC libraries? I imagine that 700k reads for mouse genome is nowhere near being sufficient to call peaks and/or try to generate bigwig coverage files for visual inspection? Is there anything else I should be looking at prior to submission for HiSeq sequencing? I will greatly appreciate any feedback/suggestions from you.
Thank you!
I have recently prepared a pool of 9 ATAC-seq libraries from mouse hearts and performed a MiSeq Nano run to validate my pooling calculations, as it's difficult to accurately quantify the libraries.
From the data I’ve received (~1 million 150bp PE reads), it looks like most of the samples were pooled correctly (in terms of read number yield).
The alignment rates (~75-80% of uniquely mapping reads, ~15% mapping more than once) and mitochondrial contamination (less than 5%) seem fine to me as well.
What I was wondering is whether there is any other information that I can extract out of this run to be confident in my ATAC libraries? I imagine that 700k reads for mouse genome is nowhere near being sufficient to call peaks and/or try to generate bigwig coverage files for visual inspection? Is there anything else I should be looking at prior to submission for HiSeq sequencing? I will greatly appreciate any feedback/suggestions from you.
Thank you!
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