Patent ID: 8566039

Claim:
A computer-implemented method for determining a quantitative measure for an RNA expression profile of a biological sample containing sequences of nucleotides, the method comprising: for each of a plurality of output sequences from the biological sample: receiving, information of an alignment of the respective output sequence onto a reference sequence that has a nucleotide at each of a plurality of nucleotide positions, the alignment aligning the output sequences to specific nucleotide positions of the reference sequence, wherein at least a portion of the output sequences are derived from RNA, and wherein the reference sequence includes at least a portion of a genome; calculating a count histogram for the reference sequence based on the alignment of the plurality of output sequences onto the reference sequence, the count histogram including a respective coverage count for each nucleotide position of the reference sequence, wherein calculating the count histogram includes: for each nucleotide position of the reference sequence: determining, the corresponding coverage count for the respective nucleotide position by determining the number of output sequences that align to the respective nucleotide position of the reference sequence; locating a first contiguous region in the count histogram where the coverage count for each nucleotide position in the first contiguous region is equal to or greater than a threshold; and calculating a first abundance score for the first contiguous region, wherein an abundance score includes an average of the coverage count for each nucleotide position in a contiguous region; wherein the method is performed by a computer.