edgeCounter

Description

Given a BAM alignment file, each read pair will have two edges. edgeCounter counts the number of read pair edges that overlaps within a set of genomic ranges. To assist with constructing/importing genomic ranges, edgeCounter provides minimal dependency, easy-to-use functions for importing genomic ranges from existing BED or BED-like files (e.g., MACS2 narrowPeak) and constructing genomic ranges by manually inputting specific ranges. While a complete vignette showing ATAC sequencing quantification is included, edgeCounter is expected to be directly applicable to other sequencing applications where alignment edges/ends, rather than full-length alignments themselves, are of interest.

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• Ye Yuan author maintainer