7.5 Further processing of aligned reads
After alignment, some further processing might be necessary. However, these steps are usually sequencing protocol specific. For example, for methylation obtained via bisulfite sequencing, C->T mismatches should be counted. For gene expression measurements, reads that overlap with transcripts should be counted. These further processing tasks are either done by a specialized alignment-related software or can be done in R in some cases. We will explain these further processing steps when they become relevant in the context of the following chapters.