5. cDNA / Transcriptome Sequencing Appendix
: 5.3 Transcriptome Mapping Concepts
5.3
Transcriptome Mapping Concepts
5.3.1 Mapping cDNA Reads to a Transcriptomic Reference
5.3.2 Mapping cDNA Reads to a Genomic Reference
5.3.1
Mapping cDNA Reads to a Transcriptomic Reference
Reads derived from cDNA samples can be mapped to a collection of reference sequences representing the set of transcripts that might be found in the sample. Often this collection of reference sequences is a list of known or putative transcripts (such as refMrna.fa from UCSC). Some of the applications that can be facilitated by such a mapping include the detection of novel SNPs within known transcripts and the profiling of expression levels for known transcripts and genes.
Many of the reads from cDNA sample may map uniquely to only one transcript. Uniquely mapped reads can be used for SNP detection and for profiling transcript levels. However, because some exons may be shared by many transcripts (e.g. splice-variants from a single gene), reads covering such exons may map equally well to many transcripts. In such cases, it may not be possible to assign the reads to any single transcript reference. Nonetheless, when mapping to transcriptomic references, it is often possible to determine the number of reads that map to a single gene even when reads cannot be mapped uniquely to a single transcript produced by the gene.
