scripts

Scripts

Abundance after cupcake merge

This script combines the individual FL counts of sample 1, sample2, and sample 3 after cupcake merge to create the FL column required for SQANTI3.

Add color to GTF

This script is used to color the transcript and ORF isoforms according to their IsoQuant classification.

Convert GTF to colored BED

This script contains the information on how add_color_to_gtf.py was used to create the visualisatiions for the UCSC genome browser.

NCBI human protein coding genes and NCBI gene results to Python

These scripts are used to perform the Gene Ontology enrichment analysis in Figure 1D.

IsoQuant to SQANTI3 converter

This script converts the IsoQuant output into a SQANTI3-like classification file that is required for the long-read proteogenomics pipeline by Miller et al.

Replace gene identifier

This script is used to add a gene name column to the IsoQuant output based on the gene id column.

Utils (R)

This script contains the combined_cds_utr_gtffile function that is used to create the IsoQuant track in Figure 4.

Utils (Python)

This script contains the following Python functions:

• ird_gene_list reads the RetNet genes and stores them in a list
• replace_geneid_by_symbol replaces a gene ID by the gene symbol
• replace_geneid_by_symbol replaces the gene ID by the gene symbol for a pandas dataframe
• overlap3 creates a Venn diagram for a dataset with three different samples
• digest digests a protein sequence with the specified enzyme
• refine_source defines if a peptide is multi-mapping or not