== Using ngsplot to make stacked heatmaps and profiles of genes or genomic regions (like ChIP-seq peaks) ==
 [[https://github.com/shenlab-sinai/ngsplot/wiki | ngsplot]] is a great tool to make heatmaps and profiles of mapped reads (i.e. bam files of RNA-seq, ChIP-seq etc) across genes, transcription starts sites or other regions of interest.
 The regions used can be genes included on the ngsplot annotation or custom regions included on a bed file.

* Here is an example of a ngsplot command using custom regions
{{{
        bsub ngs.plot.r -G hg19 -R bed -L 3000 -C config.txt -O Peak_Summits

        * Example of the tab delimited config.txt file

         TF1.sorted.bam	      peaks.SUMMIT.bed	"TF1" 
         TF2.sorted.bam	      peaks.SUMMIT.bed	"TF2" 
         Pol2.sorted.bam      peaks.SUMMIT.bed	"Pol2" 
}}}
* Here is an example of a ngsplot command using gene annotations within the ngsplot package

{{{

}}}