---
title: "How do I analyze Fiber-seq data?"
slug: "how-do-i-analyze-fiber-seq-data"
updated: 2026-03-24T19:13:30Z
published: 2026-03-24T19:13:30Z
canonical: "support.epicypher.com/how-do-i-analyze-fiber-seq-data"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://support.epicypher.com/llms.txt
> Use this file to discover all available pages before exploring further.

# How do I analyze Fiber-seq data?

Analyzing Fiber-seq data involves two main steps: standard base calling and alignment using PacBio or ONT pipelines, followed by Fiber-seq-specific analysis. Once reads are processed, the [fibertools](https://fiberseq.github.io/fibertools/fibertools.html) package provides QC metrics, 6mA pileups, and footprinting insights to evaluate chromatin features. These tools ensure your data captures biologically meaningful accessibility and nucleosome organization.

**Base Calling and Alignment**

- Use platform-specific pipelines from PacBio or ONT.
- ONT users can perform real-time base calling with MinKNOW before Fiber-seq-specific analysis.

**Fiber-seq Analysis**

- The fibertools package provides:
  - QC metrics
  - 6mA pileups
  - Protein footprinting inference
- QC outputs include:
  - Methylation Sensitive Patches (MSPs): Should average 20–90 bp
  - Autocorrelation Plots: Should show nucleosome footprints around ~147 bp

**Key Resource Links:**

- [Fiber-seq GitHub](https://github.com/fiberseq)
- [Quick start guide](https://fiberseq.github.io/quick-start.html)
- [PacBio Analysis Tools](https://www.pacb.com/products-and-services/data-analysis/)
- [ONT Analysis Resources](https://nanoporetech.com/document/data-analysis)
- Publicly available datasets for test use:
  - PacBio: [https://www.ncbi.nlm.nih.gov/sra/SRX28885063%5baccn%5d](https://www.ncbi.nlm.nih.gov/sra/SRX28885063%5baccn%5d)
  - ONT: [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA956114](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA956114)1

**References**
    1. Jha et al. [DNA-m6A calling and integrated long-read epigenetic and genetic analysis with *fibertools.*](https://pmc.ncbi.nlm.nih.gov/articles/PMC11610455/) J Exp Med 217 (2020).