read_distribution.py

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Provided a BAM/SAM file and reference gene model, this module will calculate how mapped reads were distributed over genome feature (like CDS exon, 5’UTR exon, 3’ UTR exon, Intron, Intergenic regions). When genome features are overlapped (e.g. a region could be annotated as both exon and intron by two different transcripts) , they are prioritize as: CDS exons > UTR exons > Introns > Intergenic regions, for example, if a read was mapped to both CDS exon and intron, it will be assigned to CDS exons.