Session Ready
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.