Multimapped Reads

[ky66]

How does this package deal with multi-mapped reads?

[r78v10a07]

The model to describe the genomic features used for a gene is created from the GTF provided by the user. TPMCalculator performs two transformations which are executed on the genomic coordinates generating regions for the genes that include the exons and ‘pure’ intron regions as shown in Supplementary Figure S1. The first transformation creates overlapped exons for all alternative spliced forms of the gene. A single gene model is generated with unique exons and introns which includes the sequence of all exonic regions. The second transformation creates a list of pure intron regions that replace those generated by the first transformation. We should emphasize that only the intron regions included are from regions that are not from overlapping exons of other genes. Reporting TPM values for these unique introns permits further identification of alternative splicing events such as intron retention. Additionally, a set of non-overlapped gene features (exons and introns) are generated and used for TPM calculation.