•Alignment to genome
–Allow reads from unannotated loci, introns et cetera to align to
their correct locations… potential for new biological
insights
•Alignment to transcriptome
–Computationally inexpensive
–Spliced (exon junction) reads map correctly
–Pairing distance and junction reads may help
distinguish individual isoforms (informative/unique regions
of transcripts)
•Assembly
–Can provide a more long-range view of transcripts
–Allows detection of chimeric transcripts and resolution of ‘breakpoints’
–May not necessarily need a genome