Exercise

Filtering reads on the go!

What if, from all of the reads in a file, you are only interested in some of those reads? You can use a filter!

Let's say that you are interested only in those reads that start with the pattern "ATGCA". A tiny filtering function can do the job, making use of the srFilter() function:

myStartFilter <- srFilter(function(x) substr(sread(x), 1, 5) == "ATGCA")

This function, which has been created for you, takes a ShortRead derived object as an input and outputs the reads starting with the pattern "ATGCA". Let's put this function to use!

Instructions 1/2

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  • Check the class of fqsample.
  • Use the filter myStartFilter() on fqsample and save the result in selectedReads.
  • Check the class of selectedReads.