extract_splice_sites {Rhisat2} | R Documentation

## Extract splice sites from annotation

### Description

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`.

### Usage

    extract_splice_sites(features, outfile, min_length = 5)

### Arguments

`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.

### Value

Nothing is returned, but the splice junction coordinates are written to `outfile`.

### Author(s)

Charlotte Soneson

### References

Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12:357-360 (2015).

### Examples

    tmp <- tempfile()
    extract_splice_sites(features=system.file("extdata/refs/genes.gtf",
                                              package="Rhisat2"),
                         outfile=tmp, min_length=5)

[Package Rhisat2 version 1.4.0 Index]