bamPlot_turbo

• Overview
• Install
• Usage
• Examples
  • Plotting a single locus

# Overview * bamPlot_turbo is a set of scripts designed to create publication quality vector graphic plots of read density from nextgen sequencing data across specific genomic loci. * Read data must be in the form of sorted and indexed [BAM](http://samtools.sourceforge.net/) files * Input regions can either be specified individually e.g. `chr1:+:1-1000` or as a batch via a [.gff](http://genome.ucsc.edu/FAQ/FAQformat.html#format3) file. * Reference gene annotations are also plotted. (Currently, only HG18,HG19,MM8,MM9 are supported) * Additional reference regions can be plotted when provided in [.bed](http://genome.ucsc.edu/FAQ/FAQformat.html#format1) format # Install * bamPlot_turbo is part of the bradnerLab pipeline module. Install instructions under construction # Usage * bamPlot_turbo is called from the command line using python ./bamPlot_turbo.py ``` Usage: bamPlot_turbo.py [options] -g [GENOME] -b [SORTED BAMFILE(S)] -i [INPUTFILE] -o [OUTPUTFOLDER]

Options: -h, --help show this help message and exit -b BAM, --bam=BAM Enter a comma separated list of .bam files to be processed. -i INPUT, --input=INPUT Enter .gff or genomic region e.g. chr1:+:1-1000. -g GENOME, --genome=GENOME specify a genome, HG18,HG19,MM8,MM9 are currently supported -o OUTPUT, --output=OUTPUT Enter the output folder. -c COLOR, --color=COLOR Enter a colon separated list of colors e.g. 255,0,0:255,125,0, default samples the rainbow -s SENSE, --sense=SENSE Map to '+','-' or 'both' strands. Default maps to both. -e EXTENSION, --extension=EXTENSION Extends reads by n bp. Default value is 200bp -r, --rpm Normalizes density to reads per million (rpm) Default is True -y YSCALE, --yScale=YSCALE Choose either relative or uniform y axis scaling. options = 'relative,uniform' Default is relative scaling -n NAMES, --names=NAMES Enter a comma separated list of names for your bams -p PLOT, --plot=PLOT Choose either all lines on a single plot or multiple plots. options = 'single,multiple' -t TITLE, --title=TITLE Specify a title for the output plot(s), default will be the coordinate region --save-temp If flagged will save temporary files made by bamPlot --bed=BED Add a comma separated list of bam files to plot

<a name="Examples"/>
# Examples
<a name="single_locus_example">
#### Single locus plot
* plotting reads from two datasets at a single genomic region

python ./bamPlot_turbo.py -g 'hg18' -b $BAM1,$BAM2 -i 'chr1:+:100900000-100980000' -r -y 'UNIFORM' -t 'VCAM1' --bed $BED1 -o './'