ATAC-Seq FAQ
Frequently asked questions about ATAC-seq analysis
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
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
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
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
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
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
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
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
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
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