extract_splice_sites {Rhisat2} | R Documentation |
This function extracts splice sites from an annotation object (a gtf/gff3
file, a GRanges
object or a TxDb
object) and saves them in a
text file formatted such that it can be directly used with HISAT2, by
providing it as the argument known-splicesite-infile
.
extract_splice_sites(features, outfile, min_length = 5)
features |
Either the path to a gtf/gff3 file containing the genomic features, a GRanges object or a TxDb object. |
outfile |
Character scalar. The path to a text file where the extracted splice sites will be written. |
min_length |
Integer scalar. Junctions corresponding to introns below this size will not be reported. The default setting in HISAT2 is 5. |
Nothing is returned, but the splice junction coordinates are written
to outfile
.
Charlotte Soneson
Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12:357-360 (2015).
tmp <- tempfile() extract_splice_sites(features=system.file("extdata/refs/genes.gtf", package="Rhisat2"), outfile=tmp, min_length=5)