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
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Load ShortRead
library(___)
# Check quality
___(___)