Hey! I have performed an alignment of my reads (paired end) using Bowtie2. I would like to know which region of the genome is most highly covered.
As per my knowledge this can be done using mpileup or Bamcov or visualize the bam file in IGV. But, I want to specifically see which genes are the most highly covered and not just regions of high coverage.
Is there a way bam files can be mapped on gff files or is there any other approach to this.
Looking forward to replies!!