When we have a new set of sequence reads to work with, whether that be from a new experiment or a database, we need to perform a quality control step that will remove any sequence adapters, remove reads with a poor sequence, or trim down a poor sequence, as appropriate. In this recipe, we'll look at doing that within R using the Bioconductor ShortRead package.
Performing quality control and filtering on high-throughput sequence reads
Getting ready
You'll need the ShortRead package and you'll need to run the code for the Finding experiments and reads from SRA/ENA recipe in this chapter. Two files are created in the last step of that recipe and we'll use one of those. Once that code is run, the file should...