Au Lab

Utilities

Finds the junctions that do not exist in a reference file. If you wish to find the junctions that differ between two bed files, you should run this tool twice with each file as reference.

usage: findNovelJunctions <ref_refFlat.txt> <junction.bed>
or findNovelJunctions <junction1.bed> <junction2.bed>

Convert genepred file to fasta.

usage: python genepred2FASTA.py <refFlat.txt> <genome_list_filename>

Convert genepred file to gtf file.

usage: python genepred2gtf.py <genepred_file> <refFlat.txt>

Convert to genepred file to bed file.

usage: python gpd2bed.py <gpd_file>

Find novel isoforms in .gpd file (such as predicted isoforms from IDP).

usage: python novel_genepred.py <ref_refFlat_file> <tag_refFlat_file> <output_file>