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Exercise

More filtering!

Awesome! Now that you've had some practice with filtering reads, let's use the function polynFilter(). This function selects reads that contain less than a given number of duplicate nucleotides. For example, polynFilter(threshold = 20, nuc = c("A")) will select all reads that contain less than 20 A's. The parameter nuc is a character vector containing IUPAC symbols for nucleotides or the value "other" for all non-nucleotide symbols.

The fqsample object is available in your workspace.

Instructions 1/3
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  • Extract the sequences from the ShortRead object fqsample using the appropriate function.
  • Create a filter called myFil using polynFilter with the following parameters:
    • A threshold of 3 nucleotides.
    • A character vector nuc equal to "A".
  • Check the newly created filter by printing it to the console.