ngsplot ngs.plot tutorial

#!/bin/sh
#
#SBATCH --job-name=testJob
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --partition=dragon-default
#SBATCH --ntasks-per-node=1
#SBATCH --mem=8192
#
# Display all variables set by slurm
env | grep "^SLURM" | sort

## run with command: sbatch NGSPLOT_test.sh

#module load gcc/4.7.4
#module load  compilers-extra
#module load samtools/1.1
#module load bwtool/1.0

module purge
module load slurm
module load gcc/4.7.4
module load R/3.1.1
module load ngsplot

dataDir="/home/alamt/HMCan_test/"
workDir=/home/alamt/NGSPLOT/

cd $workDir


hg19size=hg19.chrom.sizes

tfName="MEF_2A"

bedFile="F5_robust_DPI_TSS_500_upstream_500_downstream_nonCoding_only.bed"


###############################
##### 1. Run ngs.plot.r
##### Mandatory parameters:
#  -G   Genome name. Use ngsplotdb.py list to show available genomes.
#  -R   Genomic regions to plot: tss, tes, genebody, exon, cgi, enhancer, dhs or bed
#  -C   Indexed bam file or a configuration file for multiplot
#  -O   Name for output: multiple files will be generated
##### Optional parameters related to configuration file:
#  -E   Gene list to subset regions OR bed file for custom region
#  -T   Image title
###############################

ngs.plot.r  -G hg19 -R bed  -C $dataDir/wgEncodeHaibTfbs/wgEncodeHaibTfbsGm12878Mef2aPcr1xAlnRep1.bam:$dataDir/wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputStdAlnRep1.bam  -O  MEF_2A_NGSPLOT.txt -T $tfName -E $bedFile