[Bioc-sig-seq] Plotting Coverage for inhouse genome

[Pratap, Abhishek]

Hi All

After taking an exciting BioC course at FredHutch recently, I am trying
to dive into BioC world to make more sense of NGS data. I would also
like to thank the entire BioC team present there. You guys were simply
great. I appreciate you all patiently answering tons of questions and
taught some of the cool things we can do with BioC packages.

For my current problem I would like to generate coverage plots for a
small bacterial genome. I have the reads imported as a AlignedRead
object and I am not sure how to proceed next. The help for the
"coverage" method didn't get me very far. I am looking for some pointers
to help me resolve the following questions.

1. How to create a RLE list from the AlignRead object using coverage
method ? 
2. Do I need to pack my reference genome as BSgenome data package in
order to do this ? If yes I just have the sequence and no group II mask
file.
3. Finally how to plot a RLE list.

Thanks!
-Abhi