process_junction_table {megadepth} | R Documentation |
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.
process_junction_table(all_jxs)
all_jxs |
A |
Processed junctions in a STAR-compatible format.
## 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