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Exercises and solutions for Chapter 7

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]

solution:


folder=(system.file(package="QuasR", "extdata"))
library(Rqc)
folder = system.file(package="ShortRead", "extdata/E-MTAB-1147")

# feeds fastq.qz files in "folder" to quality check function
qcRes=rqc(path = folder, pattern = "^chip", openBrowser=FALSE)
rqcCycleQualityBoxPlot(qcRes)
  1. 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]

solution:

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

solution:

#coming soon