Further material for Pass et. al 2017, "Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis"
BAM2SizePlot.py script used for 2D and 3D figure generation from Paired-End sequence date from MNase digested genomic DNA, utilising the plotly visualisation package.
BAM2SizePlot.py -h
usage: BAM2SizePlot.py [-h] [-i I] [-d D] [-o O] [-B B] [-b B] [-g G] [-G G]
[-e E] [-s S] [-S S] [-q Q] [-r R] [-p P] [-z Z] [-t]
Import Bam file and extract defined region for 2D or 3D plotting
optional arguments:
-h, --help show this help message and exit
-i I Input a Bam file or a list of comma-separated Bam files to merge
(format: one.bam,two.bam,three.bam)
-d D Optional: Directory where bamfiles are (saves on typing!)
-o O Output prefix
-B B One individual set of co-ordinates in bed format
(Chr1:1000-1510)
-b B Bed file of regions to extract (Bed file)
-g G Gene transcript to get positional information from | REQUIRES
GTF FILE (-G)
-G G gtf file to get gene model information from | REQUIRES
GENE/TRANSCRIPT ID
-e E Integer for upstream/downstream extension
-s S Minimum size of particle
-S S Maximum size of particle
-q Q Integer for rounding counts (fragment size, default: 10)
-r R Integer for rounding counts (bases, default: 50)
-p P Choose plot type (2D or 3D, default:2D)
-z Z Change zmax for plot (Mainly to look at low abundance things)
(Default 1000, 'None' allows dynamic assignment)
-t Use default co-ordinates for testing
