This repository contains scripts and files accompanying the manuscript IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection.
The LRP pipeline previously described by our group was run on this dataset using the Nextflow workflow.
git clone https://
.com/sheynkman-lab/Long-Read-Proteogenomics
cd Long-Read-Proteogenomics
nextflow run main.nf --config conf/test_with_sqanti.config
Raw sequencing data files can be found in the National Institutes of Health (NIH) National Library of Medicine’s Sequence Read Archive with the project accession number PRJNA1090880
Mass spectrometry raw files, Proteome Discoverer PSM result files, and Tomahto result files have been deposited to the ProteomeXchange Consortium via the PRIDE archive using accessions PXD050904 and PXD050909. Data will become available upon publication of the manuscript in JASMS.
Analysis of the mass spectrometry data was conducted using custom R scripts. Associated scripts and supporting files can be found in /MassSpectrometryAnalysis.
The R script used to create area-proportional Venn diagrams comparing the DDA and Tomahto results can be found in /scripts/DDA_vs_Tomahto.Rmd.
The BED files used to create the UCSC Genome Browser track that accompanies this manuscript can be found in /TrackRepository. All scripts used to create these files using custom python scripts and Pogo can be found under /TrackRepository/scripts.