bam_to_junctions {megadepth} | R Documentation |
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.
bam_to_junctions( bam_file, prefix = file.path(tempdir(), basename(bam_file)), all_junctions = TRUE, junctions = FALSE, long_reads = FALSE, overwrite = FALSE )
bam_file |
A |
prefix |
A |
all_junctions |
A |
junctions |
A |
long_reads |
A |
overwrite |
A |
A character(1)
with the path to the output junction tsv file.
## 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