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Filter BED on splice junctions (version 0.0.1)

BED file:

e.g. tophat junctions.bed run without GTF option or no-novel-junctions

reference bed file:

e.g. tophat junctions.bed run with GTF option and no-novel-junctions

Extend the start position:

The number of base pairs to extend the start of the exon before the junction position

Extend the end position:

The number of base pairs to extend the end of the exon after the junction position

Filter BED on splice junctions

Filter out lines of a BED file that have junctions that are in in the reference bed file of known junctions. The start position of the exon preceding the junction and the end position of the exon after the junction can be extended. This is to compensate for alignments that may not include enough of the exons surrounding the junctions.

A typical application would be to run tophat twice, once with the --GTF and --no-novel-juncs options for well known splice junctions, then a second time without those options to also include novel splice junctions.

This application would filter out the well splice known junctions from the run intended to find all splice junctions including novel ones.