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  • 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 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!

  • #2
    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.

    Comment


    • #3
      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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