bam_to_junctions: Extract junctions from a BAM file
In LieberInstitute/megadepth: megadepth: BigWig and BAM related utilities

View source: R/bam_to_junctions.R

bam_to_junctions

R Documentation

Extract junctions from a BAM file

Description

Given a BAM file, extract junction information including co-ordinates, strand, anchor length for each junction read. For details on the format of the output TSV file, check https://github.com/ChristopherWilks/megadepth#junctions.

Usage

bam_to_junctions(
  bam_file,
  prefix = file.path(tempdir(), basename(bam_file)),
  all_junctions = TRUE,
  junctions = FALSE,
  long_reads = FALSE,
  filter_in = 65535,
  filter_out = 260,
  overwrite = FALSE
)

Arguments

`bam_file`	A `character(1)` with the path to the input BAM file.
`prefix`	A `character(1)` specifying the output file prefix. This function creates a file called `prefix.jxs.tsv`. By default, the prefix is the BAM file name and the file is created in the `tempdir()` and will be deleted after you close your R session.
`all_junctions`	A `logical(1)` indicating whether to obtain all junctions.
`junctions`	A `logical(1)` indicating whether to obtain co-occurring jx coordinates.
`long_reads`	A `logical(1)` indicating whether to increase the buffer size to accommodate for long-read RNA-sequencing.
`filter_in`	A `integer(1)` used to filter in read alignments. See https://github.com/ChristopherWilks/megadepth#bamcram-processing and https://samtools.github.io/hts-specs/SAMv1.pdf for further documentation on how to apply this parameter.
`filter_out`	A `integer(1)` used to filter out read alignments. See https://github.com/ChristopherWilks/megadepth#bamcram-processing and https://samtools.github.io/hts-specs/SAMv1.pdf for further documentation on how to apply this parameter.
`overwrite`	A `logical(1)` specifying whether to overwrite the output file(s), if they exist already.

Value

A character(1) with the path to the output junction tsv file.

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)

## Path to the output file generated by bam_to_junctions()
example_jxs

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