I have BAM files (RNA-Seq data, 75 bp reads) from alignment to Zebrafish genome. I know how to plot all reads in the BAM file on each chromosomes, using gviz. However, I want to plot only the reads that do not map to any known Genes, (exons or introns), rRNA, tRNA, etc. Specifically I am interested in the reads that map to intergenic regions.
I have used gviz to plot all the reads, but could not find a way to plot the reads that mapped to intergenic regions. Is there an easier way or any package suggestions?
p.s. I am planing to extract reads that do not map to ENSEMBL genes (using GTF file) and then plot them on the chromosomes? Is there a way to extract those reads that do not mapped to ENSEMBL genes from the BAM files?
thanks in advance.