This function extracts splice sites from an annotation object (a gtf/gff3
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
extract_splice_sites(features, outfile, min_length = 5)
Either the path to a gtf/gff3 file containing the genomic features, a GRanges object or a TxDb object.
Character scalar. The path to a text file where the extracted splice sites will be written.
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
Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12:357-360 (2015).
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