tagmapAnalyseR

Version 1.0.0, released 20 April 2022.

Stand-alone package integrated into transposon mapping pipeline tagmap_hopping for Tagmentation-Based Mapping (Tagmap) data, as well as stand-alone functionality.

Background

TagmapAnalyseR is a module inside the tagmap_hopping pipeline, and is particularly responsible to map (processed) TagMap reads to genomic locations and figure out where transposons (e.g. PiggyBac or Sleeping Beauty) integrated into the genome. TagmapAnalyseR combines several tricks to derive a consensus mapping location for integrations are read coverage may be ambiguous towards the precise location. More details can be obtained from the author upon request (methods section in thesis).

Usage

Dependencies for pipeline are described in the respective repository, see its map_insertions.R script for practical application of tagmapAnalyseR.

Installation

devtools::install_github("https://github.com/krademaker/tagmapAnalyseR")

Load processed read coverage of (putative) integrations

dt <- tagmapAnalyseR::readPutativeInsertions(input)

Obtain integrations with ambiguous read coverage

ambiguous <- tagmapAnalyseR::findAmbiguousInsertionSites(dt, padding = (nchar(overhang_sequence)*2)+2)

Map integrations

mapped <- tagmapAnalyseR::mapInsertionSites(dt = dt,
                                            bam = bam_path,
                                            overhang = overhang_sequence,
                                            samtoolsPath = samtools_path,
                                            depth = as.integer(minimal_read_depth),
                                            ambiguousInsertions = ambiguous)

Contact / Support

Reach out through the issues section or reach out directly to the author.