question: Name the algorithms for counting multi-mapping reads
answer: RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used (drop duplicated genes, distribute uniformly the reads, or estimate expression), but all of them provide biased results. Mmquant is a tool for computing gene expression, including duplicated genes. If a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Other methods have been developed that use weighted allocation of read counts but these methods treat the different types of multi-reads equivalently. For instance a hierarchical approach was developed for allocation of read counts that first resolves ambiguities among genes, then among isoforms, and lastly between alleles. The model has been implemented in EMASE software (Expectation-Maximization for Allele Specific Expression) to estimate total gene expression, isoform usage and ASE based on this hierarchical allocation.