Repository filter_bed_on_splice_junctions
Owner: jjohnson
Synopsis: Filter out lines of a BED file that have junctions that are in in the reference bed file of known 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 unctions.  

This application would filter out the well splice known junctions 
from the run intended to find all splice junctions including novel ones.
Type: unrestricted
Revision: 0:915e5c5e02e6
This revision can be installed: True
Times cloned / installed: 1126

Contents of this repository

Name Description Version Minimum Galaxy Version
that are not in a reference bed file 0.0.1 any

Categories
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis