modbedtools 0.1.0

Generate modbed track files for visualization on WashU Epigenome Browser

modbedtools

Requires Python >= 3.6

A python command line tool to generate modbed files for visualization on WashU Epigenome Browser

This tool parses MM/ML tag from BAM files generated from 3rd generation sequencing platform like Oxford Nanopore and PacBio devices using the pysam package.

modbed format

chr11   5173273 5195306 -110,-266,-1459,-1780,-1840,-1842,-1848,-1865,-1928,-1936,... -396,-1543,-3222,-4195,-4319,-4692,-5352,-5366,-5523,-5838,...
chr11   5174507 5194585 223,605,607,613,630,693,701,936,1761,3369,...  307,544,1280,2017,2859,2994,3116,3249,3790,3935,...
chr11   5174543 5196481 187,271,508,570,576,593,901,1729,2826,3216,...     568,656,664,1985,2961,3083,3703,4115,4286,4882,...

Each row in this bed-based format is a long read, the columns are:

• chromosome
• start position of this read
• end position of this read
• methylated/modified base positions, relative to start
• unmethylated/unmodified/canonical base positions, relative to start

All positions are 0 based.

commands

modbedtools -h                                                                                    
usage: modbedtools [-h] [--version] {bam2mod,addbg} ...

Python command line tool to generate modbed files for visualization on WashU Epigenome Browser.

optional arguments:
  -h, --help       show this help message and exit
  --version, -v    show program's version number and exit

subcommands:
  valid subcommands

  {bam2mod,addbg}  additional help
    bam2mod        convert bam to modbed
    addbg          add backgroud bases given modified bases and reference sequence

(files for testing can be found in the test folder in this repository)

bam2mod

convert bam files with MM/ML tags to modbed format.

modbedtools bam2mod -h             
usage: modbedtools bam2mod [-h] [-c CUTOFF] [-o OUTPUT] bamfile

positional arguments:
  bamfile               bam file with MM/ML tags

optional arguments:
  -h, --help            show this help message and exit
  -c CUTOFF, --cutoff CUTOFF
                        methylation cutoff, >= cutoff as methylated. default: 0.5
  -o OUTPUT, --output OUTPUT
                        output file name, a suffix .modbed will be added. default: output

examples:

modbedtools bam2mod hifi-test.bam -o hifi

modbedtools bam2mod remora-test.bam -o remora

addbg

For data provided methylated bases, given a reference genome fasta sequence, add the unmethylated bases from genome sequence as background, this assumes all other specified bases from genome are unmethylated/unmodified.

The input file should be in bed format, the last column saves the comma separated relative base position with modification (0 based).

example input:

chr11   5193360   5212743   {middle columns can be anything or none}    21,273,296,307,440,461,475,688,689,694,863...

the data above is adopted from one of the Fiber-seq data from John Stamatoyannopoulos lab.

modbedtools addbg -b A fiber_seq_HBG_DS182418_2022dec07.bed12 chr11.fa.gz -o fibe-seq-HBG_DS182418

track formating

Tabix is used to compress and index the modbed files generated in last steps.

example:

bgzip hifi.modbed
tabix -p bed hifi.modbed.gz

Then the .gz and .gz.tbi files can be placed into any web server for hosting and the URL to the .gz file can be used for Visualization in WashU Epigenome Browser.