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¶
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.