How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
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12 weeks ago
cyril-cros ▴ 950

Hi, my lab plans to do scATAC-seq in a non model organism. We have generated a series of preliminary bulk ATAC-Seq runs from the same biological sample in many different technical conditions (dissociation methods, buffers, incubation time with transposase etc..., ~20 conditions). I ran a pipeline to process these results which relies on Bowtie for the alignments / MACS2 for peak calling. At this point, the alignment values are not too bad, I can open a genome browser to display peak data tracks, and the peaks look mostly consistent across runs. I have various reports (FastQC alignment rates etc...). Due to the organism I don't have well annotated TSS or a list of regions to blacklist.

What criteria should I use to select the "best" experimental conditions?

  • alignment rates before/after trimming
  • (normalized across runs) peak height/width
  • consistency between peak positions across runs
  • attempt to determine TSSs from ATAC-Seq and align peaks across that (but that's a circular argument)
  • FRiP scores
ATAC-seq • 172 views

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