ATAC QC Filtering Tiling Regions

[astarr97]

Hello,

We did a very shallow sequencing run of ~8 million reads (before mapping etc.) spread over 20 bulk atac samples from 5 different cell types with 3 "treatments" each (notably, our qubit seems to have been quite off so the reads are not very evenly distributed across the samples). I have been using ChrAccR to do some quality control on the data. Things look decent (nowhere near as nice as the T-cell data provided in terms of peak distribution though) except for one glaring difference between the two. In my data, we only retained 5710 50 bp tiling regions after filtering (compared to ~53,000 in the T-cell data). In addition, the initial filtering step (with the 95% cutoff) only discarded 77% of regions in my dataset (compared to ~99% in the T-cell dataset). The code I am using to run both datasets is identical except for the names of columns in the samples.tsv file. Because there are likely differences in sequencing depth and the T-cells probably have much more similar chromatin than our cell types, a direct comparison seems tricky. Essentially I am wondering: is this level of tiling region retention in line with what you would expect? This is the lab's first time doing ATAC-seq so we don't really have much idea; any help would be much appreciated.

Best, Alex.

PS So far my experience with ChrAccR has been very good, surprisingly painless to install and get running.