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Author: Mitchell R. Vollger

src/quick-start.md

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 # The quick start guide for analyzing Fiber-seq data
 
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 The primary tool for handling Fiber-seq data is `fibertools`, and this page provides a high level order of operations for turning you raw Fiber-seq data into useful chromatin information. The steps differ slightly depending on if you are starting with PacBio or Oxford Nanopore Technologies (ONT); however, the steps can be summarized as:
 
 - Create or filter m6A calls
 - Infer nucleosomes and modification sensitive patches (MSPs)
+- Apply the Fiber-seq QC tool
 - Align and phase the data
 - Validate your Fiber-seq BAM file
 - Apply Fiber-seq inferred regulatory element (FIRE) calling to identify peaks and create UCSC browser tracks
 
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 # Fiber-seq starting with PacBio
 
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