Completing read-to-reference alignment with external programs

The alignment of high-throughput reads is an important prerequisite for a lot of the recipes in this book, including RNAseq and SNP/INDEL calling. We looked at them in depth in Chapter 1, Performing Quantitative RNAseq, and Chapter 2, Finding Genetic Variants with HTS Data, but we didn't cover how to actually perform alignment. We wouldn't normally do this within R; the programs needed to make these alignments are powerful and run from the command line as independent processes. But R can control these external processes, so we'll look at how to run an external process so you can control them from within an R wrapper script, ultimately allowing you to develop end-to-end analysis ...

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