Snakemake workflow

Title: Extracting HERV Expression Uveal Melanoma Datasets

Bulk RNA-Seq Telescope analysis of TCGA primary uveal melanoma samples, MSKCC metastatic uveal melanoma samples, and Nilsson metastatic melanoma samples (restricted access). Input the table that include the links needed to download the raw sequencing files, output gene/HERV count matrices.

Dataset Citations

TCGA citation

Robertson, A. G., et al. (2017). "Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma." Cancer Cell 32(2): 204-220.e215.

MSKCC citation

Kraehenbuehl, L., et al. (2022). "Pilot Trial of Arginine Deprivation Plus Nivolumab and Ipilimumab in Patients with Metastatic Uveal Melanoma." Cancers (Basel) 14(11).

Nilsson citation

Karlsson, J., et al. (2020). "Molecular profiling of driver events in metastatic uveal melanoma." Nat Commun 11(1): 1894.

Workflow Graphs

To get DAG:

snakemake --profile profiles/aws --forceall --dag | dot -Tpdf > dag.pdf

To get rule graph:

snakemake --profile profiles/aws --forceall --rulegraph | dot -Tpdf > rulegraph.pdf

To get file graph:

snakemake --profile profiles/aws --forceall --filegraph | dot -Tpdf > filegraph.pdf

To run pipeline:

snakemake --profile profiles/aws/ all

To modify pipeline:

Change sample download table and method. This pipeline uses different methods to download files.

TCGA: curl EGA (Nilsson): pyega3 MSK: already obtained from collaboration with MSK IMPACT project

Usage

This is a part of Phoebe Fei's thesis: "Human Endogenous Retroviruses Profiling of Metastatic Uveal Melanoma". If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository: https://github.com/nixonlab/HERV_um_mets