Most modified region (Modification analysis)
The file ~/nanomod_course_data/yeast/subset_2.sorted.bam
contains reads from the yeast dataset longer than 30 kb
that pass through the region chrVI:150000-250000.
Our goal is to identify which of the following three regions
is the most modified:
- chrVI:220000-230000
- chrVI:150000-160000
- chrVI:190000-200000
You can solve this in whichever way you want and produce a qualitative or a quantitative solution. For the official solution, we want you to implement the steps below:
- Our molecules fall into two categories: newly-synthesized DNA with BrdU in it and DNA that was synthesized before the current cell cycle and does not have BrdU. In other words, some DNA strands contain modifications and some do not. The ones that do not contain modifications will still have some bases called as modified due to the unavoidable false-positive rate of modification callers. Form a subset of reads that contain only reads with modifications using any reasonable procedure.
- Subsample the subset formed above if you desire so.
- Calculate modification amounts for each region and identify the most modified region.