ATAC-seq

An end-to-end solution to identify regions of accessible chromatin, discover motifs + functional annotations and discover epigenetic changes between samples.

Overview

Data infrastructure and tools to answer key biological questions about the epigenetic state of your samples.

Answer Biological Questions

  • How do peaks of accessible DNA vary between different samples?

  • Are there enriched motifs or functional annotations associated with these regions?

  • Where are genomic regions of chromatin accessibility?

Go from FastQ → publication-quality results in minutes

80% cheaper than CROs

Analysis Lifecycle

Store Sequencing Data

Scalable, cloud-native storage for FastQ files. A central location to organize teams. Graphical interface for scientists + CLI for programmers

Mount S3 / GCP buckets, integrate with Illumina Basespace, drag and drop from laptops, deploy custom upload scripts from local servers

List of data within Latch

Automatic QC reports that run on data upload. Accessible on double-click to scientists.

List of data within Latch

Capture Experimental Metadata

Associate drug treatments, cell lines and other metadata with raw sequencing files in structured schemas.

Graphical control and accessibility of tables by scientists.

Screenshot showing searchable data tables in Latch graphical table interface

Project management features to organize data by experiment and biological focus.

Screenshot showing project organization of experiment metadata in Latch graphical interface

Align Reads and Call Peaks

Use the nf-core/atacseq workflow to perform QC, trimming, (pseudo) alignment. Produce a gene count matrix and QC reports.

User friendly no-code interface accessed through Latch Workflow for biologist to drag and drop fastq files to launch nf-core/atac-seq

Scale to hundreds of samples and pay for only the computing resources you use.

Scientists upload and edit graphical sample sheets to run bioinformatics workflows.

Pull in error-validated and typed metadata to fill out workflow parameters.

Explore with Peak Tracks with Managed IGV

Double-click on .bigWig, .bed, .broadPeak, .gappedPeak and other file tracks to open in IGV.Save time with pre-indexed files, sensible configuration defaults and managed IGV sessions.

Annotate Peaks with Function using Homer

Call peaks with MACS2, annotate peaks with HOMER, view aggregated reports with MultiQC

Downstream Analysis in Interactive Dashboards

Plots and analysis blocks built to answer major and general biological questions. User tested extensively with scientists. Full control over plot formatting and underlying code if needed.

Compare peaks across many different samples. Drag and drop to zoom

Interactive quality control with eg. nucleosome periods with full control over plot formatting, type, labels, etc.

Looking for an easy solution?

Eliminate manual clicking and user error with an automated plotting solution for your lab.

7-Day Free Trial

Access the leading data platform for biology.

  • A scoping call to map out your scientific workflows
  • Access a curated workspace customized to your assays and needs
  • Live 16/6 support with a Latch bioinformatics engineer
  • A hands-on onboarding session to train your team