Frequently asked questions about ATAC-seq analysis

What quality control metrics are important in ATAC-seq data?
ATAC-seq, like other next NGS types, involves numerous steps including library preparation, base calls and read mapping. Each step has to be evaluated to en...
Thu, 3 Dec, 2020 at 10:14 PM
What is the difference between coverage and read depth? How many reads do you need for ATAC-seq data?
Coverage and read depth are metrics that look at how well your library has been sequenced. Visually you can picture coverage looking at it horizontally, whi...
Thu, 3 Dec, 2020 at 10:33 PM
What is the expected duplication rate for ATAC-seq data?
Duplicate reads are generally the result of PCR duplicates during library preparation, and in the pre-processing steps those reads are marked and removed. S...
Thu, 3 Dec, 2020 at 10:38 PM
Do you need paired end data for ATAC seq?
Paired ends are preferred since they can identify both ends of the DNA fragments, which is where the transposase enzyme cuts. Paired end reads tend to offer...
Thu, 3 Dec, 2020 at 10:40 PM
I only have single end reads for my ATAC-seq analysis. Can I salvage the data?
Yes. While paired end reads are preferred, single end reads can still be used to analyze ATAC-seq data.
Thu, 3 Dec, 2020 at 10:48 PM
Do I need to filter reads of certain insert size for further analysis?
Short fragments (< 100bp) represent chromatin-free regions and should be retained. Those are regions that most likely are actively transcribed since they...
Thu, 3 Dec, 2020 at 10:53 PM
Should you see any trend in ATAC-seq alignment insert size?
Yes. DNA wraps around histones with a periodicity of ~147 base pairs. To that you need to add the base pairs needed for the Tn5 enzyme to bind, which increa...
Thu, 3 Dec, 2020 at 10:59 PM
If my samples have a different number of reads, can I call peaks on them collectively?
Yes, you can. When you have multiple samples that contain a different number of reads, the samples with the higher number of reads will be automatically dow...
Thu, 3 Dec, 2020 at 11:05 PM
What is the recommended peak setting (broad vs narrow) for ATAC-seq data?
While ATAC-seq can generate both narrow and broad regions, narrow peaks are suggested to capture nucleosome free regions. If needed, you can change this...
Thu, 3 Dec, 2020 at 11:10 PM
What is considered a good FRIP score?
FRIP stands for Fraction of Reads In Peak. It is a ratio of those reads that map in the peak of interest over the total reads. Since most reads do not fall ...
Thu, 3 Dec, 2020 at 11:15 PM