Preliminary set of scripts to take corrected_with_cds.gtf and orf_refined.fasta files through PoGo to the UCSC Genome Browser

After running the Long Read Proteogenomics Pipeline, you may want to view your proteoforms on the UCSC Genome Browser

You will want to create a conda environment I called PoGo to run these scripts. You can do this by downloading the PoGo.yml file in this repository and running the following:

conda env create -f PoGo.yml

To do this visit the folders in this repository in the following order:

1. If you have your own squence data, do this step first. If you're using GENCODE/ENSAMBL data, skip this step: GTF_FASTA_2PoGo
2. Put your peptide list in PoGo format: Peptides2Pogo
3. Run PoGo: PoGo
4. Create a track hub: TrackHub
5. Make a multiregion bed file for Genome Browser if using your own sequence data. Otherwise, skip this step: Multiregion_bed
6. (Optional) If you have a GTF file that you want to add to the UCSC Genome Browser without separating it into peptide groups, you can either upload it directly, or you can convert it to a color-coded .bed file via GTF2BED