I have a gene of interest in some RNA-Seq data, this has been aligned using STAR so as a result I have BAM files.
I am wanting to plot differential exon usage across the gene, I've viewed it in IGV and the changes I was looking for do appear to be taking place however I wanted to do this a little more quantitatively and to make a more intuitive plot showing differences in exon reads for various transcript isoforms.
Is anyone able to recommend me a particular tool for this? I am aware of software such as DEXSeq and isoformswitchanalyzeR however for now I am just looking to plot this for one particular gene rather than analyse global splicing alterations.
Many thanks in advance for any help,