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 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: