ATAC-Seq FAQ (11)

Frequently asked questions about ATAC-seq analysis

What quality control metrics are important in ATAC-seq data?

Modified on 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?

Modified on Thu, 3 Dec, 2020 at 10:33 PM
What is the expected duplication rate for ATAC-seq data?

Modified on Thu, 3 Dec, 2020 at 10:38 PM
Do you need paired end data for ATAC seq?

Modified on Thu, 3 Dec, 2020 at 10:40 PM
I only have single end reads for my ATAC-seq analysis. Can I salvage the data?

Modified on Thu, 3 Dec, 2020 at 10:48 PM
Do I need to filter reads of certain insert size for further analysis?

Modified on Thu, 3 Dec, 2020 at 10:53 PM
Should you see any trend in ATAC-seq alignment insert size?

Modified on Thu, 3 Dec, 2020 at 10:59 PM
If my samples have a different number of reads, can I call peaks on them collectively?

Modified on Thu, 3 Dec, 2020 at 11:05 PM
What is the recommended peak setting (broad vs narrow) for ATAC-seq data?

Modified on Thu, 3 Dec, 2020 at 11:10 PM
What is considered a good FRIP score?

Modified on Thu, 3 Dec, 2020 at 11:15 PM