Plot Chromsome Ideogram

usage: plot_ideogram.py [-h] [-o OUTPUT] [--organism ORGANISM]
                        [--assembly ASSEMBLY]
                        file [file ...]

positional arguments:
  file                  input bed files, the first 3 columns should be chr,
                        start, end, additional columns will be ignored.
                        Multiple files should be separated by space, you can
                        use *.bed to include all bed filess in the current
                        dir.

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        enter a job ID, which is used to make a new directory.
                        Every output will be moved into this folder. (default:
                        plot_ideogram_yli11_2019-10-17.html)
  --organism ORGANISM   possible choice: Human,Mouse,Arabidopsis thaliana
                        (default: Human)
  --assembly ASSEMBLY   GRCh38,GRCh37,GRCm38,MGSCv37,TAIR10 (default: GRCh38)

Summary

../../_images/ideogram.PNG

Input

A bed file with the first 3 columns specifying chr, start, end. Additional columns are OK, but they are ignored.

Usage

hpcf_interactive

module load python/2.7.13

plot_ideogram.py input.bed

Note that multiple bed files are accepted. They should be separated by space.

Output

An html will be emailed to you.

code @ github.