Sample information

Sample Name Label Species Experiment Type Internal Library ID Reference Genome
Panc1 cell lines Cell.line.1_replicate.1 human ATAC-seq JYH_999_1_2 hg38
Panc1 cell lines Cell.line.1_replicate.2 human ATAC-seq JYH_1000_1_2 hg38
GM19240[1] Cell.line.2_replicate.1 human ATAC-seq RMM_204_2 hg38
GM19240[1] Cell.line.2_replicate.2 human ATAC-seq RMM_205_2 hg38

Alignment metrics

Alignment statistics (by count)

Alignment statistics (by %)

Mitochondrial read fraction

FastQ Screen

Fragment size distribution

ATAC-seq fragments show a characteristic multimodal size distribution reflecting sub-nucleosomal fragments (<100bp), mono-nucleosomal (~200bp), and sometimes multi-nucleosomal fragments at ~150bp intervals beyond that.

GC content after alignment

ATAC-seq alignments tend to have high GC content due to enrichment in promoters and other regulatory sequencing.

Signal-to-noise metrics

TSSe average profile

TSSe barplot

Fraction of Reads that Overlap TSS (FROT)

Peaks metrics

Peak counts

The number of peaks called per sample. Usually ~100K-200K.

Fraction of Reads in Peaks (FRiP)

A metric of signal-to-noise ratio. We generally prefer TSSe or FROT, because these metrics are independent of peak calls which vary between libraries.

PCA

Principal Component Analysis of samples based on peak intensity (fold enrichment of calculated background from MACS2).

Correlation matrix

Spearman's correlation matrix based on peak intensity (fold enrichment of calculated background from MACS2).

Download

Batch download

Click Download file list to download a files.txt that contains the list of urls to files in this report. Then run the script bellow on the terminal: 
xargs -n 1 curl -0 -L < files.txt

Metadata table

This table contains a variety of QC metrics for each library. For more information about ATAC-seq QC metrics please see: https://www.encodeproject.org/atac-seq/