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Old 04-24-2019, 03:01 AM   #1
OlgaMikh
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Default QC of ATAC-seq libraries on MiSeq Nano

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 Iíve 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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Old 04-24-2019, 04:14 AM   #2
GenoMax
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If MiSeq nano run looks good then onwards to HiSeq sequencing. You could try analyzing the data but there is not going to be a lot you can conclude from it.
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Old 04-24-2019, 06:11 AM   #3
OlgaMikh
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Thanks for your reply! What exactly are your criteria to conclude that the sample "looks good"? Would you say that I don't need to worry if I don't see TSS enrichment in the bigwig file that I've generated from a 1 000 000 read .bam file? Thank you.
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atac-seq, miseq hiseq, quality assessment

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