bedtools genomecov -bg -strand + -ibam <file> -g <genomeindex> -scale <scalingfactor>   | awk '{print $1"\t"$2"\t"$3"\t-"$4}'     >    <name>.minus.bedGraph
bedtools genomecov -bg -strand  - -ibam <file> -g <genomeindex> -scale <scalingfactor> >  <name>.plus.bedGraph

bedGraphToBigWig <name>.plus.bedGraph    <genomeindex> ${file1%%.bam}.plus.bigWig
bedGraphToBigWig <name>.minus.bedGraph <genomeindex> ${file1%%.bam}.minus.bigWig 


scaling.brennecke.ctrl=1000000/3783827 == 0.2642827
scaling.brennecke.mutant=1000000/4529718 == 0.2207643