5. cDNA / Transcriptome Sequencing Appendix
:
5.3 Transcriptome Mapping Concepts
: 5.3.2 Mapping cDNA Reads to a Genomic Reference
5.3.2
Mapping cDNA Reads to a Genomic Reference
When mapping reads from cDNA samples to genomic reference sequences, it is often possible to detect splice variants that might not be apparent when mapping to a transcriptomic reference. Breaks in the alignments of individual reads against a region of the genome often indicate exon boundaries. Also, while one may be able to map only parts of reads derived from novel splice variants to a set of known transcripts, mapping against the genomic reference allows the identification of genomic regions not previously known to exist as part of the transcriptome. Mapping to a genomic reference only allows per-gene coverage statistics to be reported while mapping to a transcriptomic reference can facilitate the profiling of individual transcripts.
