Exercise

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.

Instructions 1/3

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  • Load ShortRead.
  • Check the quality of the sequence file fqsample.