dot-readTwoBams: Function to read in interaction-data stored in a pair of BAM...

In GenomicInteractions: Utilities for handling genomic interaction data

Description

Reads in interactions stored in a a pair of BAM files, e.g. from independent alignment of paired-end reads. Assumes that each interaction is represented by pair of PETs with the same qname (this may not always be true. Depending on data origin read qnames may end in '/1' or '/2' to denote first or second read in the pair). The function reads in files, removes unpaired reads, and pairs reads based on macthing qnames.

Usage

.readTwoBams(fn)

Arguments

fn	Character vector of two BAM files with aligned reads.

Value

list of two GRanges, storing the anchor information for each interaction

GenomicInteractions documentation built on Nov. 8, 2020, 8:19 p.m.