7.6 Exercises

For this set of exercises, we will use the chip_1_1.fq.bz2 and chip_2_1.fq.bz2 files from the QuasR package. You can reach the folder that contains the files as follows:

folder=(system.file(package="QuasR", "extdata"))
dir(folder) # will show the contents of the folder

1. Plot the base quality distributions of the ChIP-seq samples Rqc package. HINT: You need to provide a regular expression pattern for extracting the right files from the folder. "^chip" matches the files beginning with “chip”. [Difficulty: Beginner/Intermediate]

2. Now we will trim the reads based on the quality scores. Let’s trim 2-4 bases on the 3’ end depending on the quality scores. You can use the QuasR::preprocessReads() function for this purpose. [Difficulty: Beginner/Intermediate]

3. Align the trimmed and untrimmed reads using QuasR and plot alignment statistics, did the trimming improve alignments? [Difficulty: Intermediate/Advanced]