the process of mapping each read sequence to a location in a given reference genome.

Bam file

A file containing read alignments to a reference genome.

Duplicate reads

Reads that align to the exact same location. This is usually an artifact of PCR, and thus all but one of these reads are eliminated so that we don’t count the same library fragment twice.

Fastq file

A file containing sequencing reads.


The process of narrowing down the full list of sequencing reads to a final list of high quality reads for use in downstream analyses like peak calling.


A DNA fragment in the ATAC-seq library, representing a region of accessible chromatin.

Fragment size

Length of the DNA fragment in bps.

GC bias

The percentage of Guanine and Cytosine nucleotides present in a given DNA sequence.


The collection of DNA fragments generated during the ATAC-seq process.

Mapping quality

The confidence with which a read sequence can be mapped to a single location in a reference genome.


Quality Control.


The short sequences obtained from sequencing a DNA library.


Files that can be viewed on a genome browser. For more information see:

TSS Enrichment

In our experience, this is the single most important metric for ATAC-seq library quality. High quality ATAC-seq libraries should have strong enrichment for reads around Transcription Start Sites (TSS) reflecting the characteristic nucleosome free region at gene promoters.