read_multiplexed_paired_bam: Read a multiplexed, paired-end BAM file and convert to a...

In AllenInstitute/lowcat: Low Coverage Accessibility and Transcriptomics

Description

This requires that the barcodes for multiplexing are in the QNAME/read name field of the BAM file.

Usage

read_multiplexed_paired_bam(bam, barcode_start = 1, barcode_end = 32,
  read_length = 50, min_frags = 100, remove_duplicates = TRUE)

Arguments

bam	A character vector of file locations for the BAM file
barcode_start	A numeric value indicating where the barcode begins in QNAME (default = 1)
barcode_end	A numeric value indicating where the barcode ends in QNAME (default = 32)
read_length	A numeric value indicating the read length (default = 50)
min_frags	A numeric value indicating the minimum number of fragments required to retain a barcode (default = 100)
remove_duplicates	A logical value indicating whether or not to deduplicate the fragments after demultiplexing (default = FALSE)

Value

a list object containing GenomicRanges objects. List names will be barcodes.

AllenInstitute/lowcat documentation built on Oct. 30, 2019, 4:45 a.m.