I am very new to NGS analysis.
I have used BWA for mapping. My reference genome is a set of simulated long reads of E.Coli (I have used Badreads tool for this) and I have mapped short reads to this. Now I want to know for each long read which portions have been mapped. My ultimate goal is to find a distribution of the percentage mapping of the long reads. For example if the long read is 10k length and i know how much 3k length (characters of the long read) has been mapped, then I can say this long read is (10k/3k) covered by the short reads.
Is there any way to do this?