shift_bam: Shift ATAC-seq reads

In anilchalisey/chompR: ChIP and ATAC-seq data processing pipeline

Description

Tn5 transposase ahs been shown to bind as a dimer and inserts two adaptors into accessible DNA locations separated by 9bp. This function offsets reads on the positive strand by +4bp and those on the negative strand by -5bp to account for this for downstream analysis.

Usage

shift_bam(bam.file, species = c("human", "mouse"), paired = TRUE)

Arguments

bam.file	character string specifying path to bam file
species	character string specifying the name of the species. Only 'human', and 'mouse' are supported at present. [DEFAULT = human].
paired	logical, if TRUE then paired end reads

anilchalisey/chompR documentation built on May 9, 2019, 3:59 a.m.