Quantifying gene expression

Given a bam-format file with read-to-genome alignments, determine the read count corresponding to each gene. Note that a read may be mapped equally well to multiple locations in the genome. If this is the case, the read should be split equally among the possible locations (amounts to adding a count of 1/#nr_loci to the count of each of the loci).

Input:

1. Bam-files formatted files with read-to-genome alignments
2. gtf file with the genome annotation

Output: Csv-formatted file ("GeneID,Counts" similar to Input #1") Comment: In assigning reads to genes take into account the number of places to which a read can be mapped