The goal of this repository is to facilitate the readability and accessibility of read-level methylation data in a UCSC Genome Browser hub. This functionality supports any data that includes methylation information encoded as MM/ML tags. bam files are converted into bed12 format using fibertools-rs. This repository provides a solution to convert these bed12 files into bigBed format for hosting in a browser hub. The primary issue addressed is the placement of blocks at the ends of reads by fibertools, which is mandatory. However, an occasional read block entry at the end of the reads results in overlap, causing an error.

Inputs:

Inputs are generated using fibertools-rs. Specifically ft extract (documentation. The environment for fibertools can be made through conda:

conda install -c conda-forge -c bioconda fibertools-rs

fix_ftextract.sh

Removes overlapping block entries at the ends of reads. Checks if second to last and last entry overlap at all and removes last one if they do.

Usage: fix_ftextract.sh -i <input_bed> -o <fixed_bed>   

Options:   
  -i <input_bed>: Path to input bed file.   
  -o <fixed_bed>: Output path of fixed bed file.