aSMF_PB

Analysis pipeline of adenine methylation single-molecule footprinting (aSMF) experiments with PacBio sequencing. Based on the code by Stergachis et al. (2020)

Index

• Prerequisites
• Usage
• Output

Prerequisites

A conda installation with:

• bedops, datamash and samtools

The SMRT LINK Software Suite.

The C. elegans reference genome file (ce11 or later).

Usage

Take a look at the headers of each of the following scripts, modify them according to your data and run in order:

1. 01_PB_aligner.sh
2. 02_ZMW_coords_per_chrom.sh
3. 03_Kinetics.sh

Output

BED file that can be opened in a genome viewer showing the 6mA marks over a region.

Average methylation profile over a region.