Custom Gene Reference - marcrusso/DROPA GitHub Wiki

Gene Reference folder contains 4 file:

• refgene.bed : BED12 file with genes coordinates
• 5UTR.bed : BED6 file 5'UTR coordinates
• CDE.bed : BED6 file with Coding Exons coordinates
• 3UTR.bed : BED6 file 3'UTR coordinates

These files can be downloaded from UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables).

User must check that gene names have to be the same in all 4 files. To do this automatically, use the Prepare_GenomeRef.py script. Prepare_GenomeRef.py <GeneRef Folder>

If you encounter any issue in custom gene reference creation, ask us to create a new one.