Exercise

Filtering reads

In this exercise, you will further clean-up the data by removing reads with low-quality alignments. To be able to do this you need to load alignment qualities from the BAM file. These are stored in the mapq field.

Instructions

100 XP

Load reads with information about the alignment qualities attached to each read.
Identify all alignments with a quality of at least 20.
Create a boxplot comparing alignment quality distributions between the high and low-quality groups.
Remove all low-quality alignments.