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  3. ChIP-seq with Bioconductor in R

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.