8.1 Processing, alignment, quantification

• Processing & alignment see Chapter 7

After Alignment we have a BAM/SAM file which is not human readable:

BAM file

The same information can also be stored in a SAM file:

SAM file

Quantification can be performed already by alignment tools (e.g. STAR), but it can also be performed in R (Rsubread::featureCounts, QuasR::qCount, GenomicAlignments::sumarizeOverlaps)