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RnaReadCounter
The RnaReadCounter, an internal tool, counts the number of aligned reads in an RNA-Seq sample that match each annotated gene. The RnaReadCounter method is similar to "htseq-count" in “union-mode”, using a “chromsweep” algorithm.
Read counts are based on the overlapping of both reads in a pair with exons of a single gene and do not consider individual transcripts separately. Reads are not counted if they map to more than 1 genomic position or to a position with overlapping exons from more than one gene.