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Exploring sequence quality

It is your turn to perform a quality control check on the fqsample. This is an important step before starting further analyses to quickly identify data problems.

To check the encoding values for each letter in quality(), use encoding():

encoding(quality(fqsample))

For a quality assessment (QA) summary use qa():

qaSummary <- qa(fqsample, type = "fastq", lane = 1)

This qaSummary has already been created for you. QA elements can be accessed with qaSummary[["nameElement"]], where nameElement is the name of the element you wish to inspect.

This exercise is part of the course

Introduction to Bioconductor in R

View Course

Hands-on interactive exercise

Have a go at this exercise by completing this sample code.

# Load ShortRead
library(___)

# Check quality
___(___)
Edit and Run Code