Merge multiple bedfiles

usage: merge_bed.py [-h] [-o OUTPUT] [-e EXTEND] [--cut3] [--keep_info]
                    file [file ...]

merge bedfiles into one

positional arguments:
  file

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        output table name (default:
                        yli11_2023-09-12_ef80e2e7efe1.bed)
  -e EXTEND, --extend EXTEND
                        get peak center and extend by (default: 0)
  --cut3                only use first 3 columns (default: False)
  --keep_info           merge a bed6 file and randomly keep 4,5,6 columns if
                        there is overlap (default: False)

Summary

Merge multiple bed files into one bed file, pattern matching for file name is allowed.

9/12/2023 updates

Added --extend parameter so user can control output region size. If the value > 0, then the program will calculate the peak center and extend by the given length up and downstream.

Usage

Copy the bed files into working dir.

hpcf_interactive.sh

module load python/2.7.13

merge_bed.py -o union.bed *.bed

Comments

code @ github.