process_junction_table: Process junctions into a STAR compatible format

In LieberInstitute/megadepth: megadepth: BigWig and BAM related utilities

Process junctions into a STAR compatible format

Description

Parses the junctions outputted from process_junction_table() into an STAR compatible format (SJ.out) for more convenient use in downstream analyses. The columns strand, intron_motif and annotated will always be 0 (undefined) but can be derived through extracting the dinucleotide motifs for the given reference coordinates for canonical motifs. This function is an R-implementation of the Megadepth helper script, on which further details of column definitions can be found: https://github.com/ChristopherWilks/megadepth#junctions.

Usage

process_junction_table(all_jxs)

Arguments

all_jxs

A tibble::tibble() containing junction data ("all.jxs.tsv") generated by bam_to_junctions(all_junctions = TRUE) and imported through megadepth::read_junction_table().

Value

Processed junctions in a STAR-compatible format.

Examples

## Install if necessary
install_megadepth()

## Find the example BAM file
example_bam <- system.file("tests", "test.bam",
    package = "megadepth", mustWork = TRUE
)

## Run bam_to_junctions()
example_jxs <- bam_to_junctions(example_bam, overwrite = TRUE)

## Read the junctions in as a tibble
all_jxs <- read_junction_table(example_jxs[["all_jxs.tsv"]])

## Process junctions into a STAR-compatible format
processed_jxs <- process_junction_table(all_jxs)

processed_jxs

LieberInstitute/megadepth documentation built on Dec. 14, 2024, 3:30 p.m.