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.
Robertson, A. G., et al. (2017). "Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma." Cancer Cell 32(2): 204-220.e215.
Kraehenbuehl, L., et al. (2022). "Pilot Trial of Arginine Deprivation Plus Nivolumab and Ipilimumab in Patients with Metastatic Uveal Melanoma." Cancers (Basel) 14(11).
Karlsson, J., et al. (2020). "Molecular profiling of driver events in metastatic uveal melanoma." Nat Commun 11(1): 1894.
snakemake --profile profiles/aws --forceall --dag | dot -Tpdf > dag.pdf
snakemake --profile profiles/aws --forceall --rulegraph | dot -Tpdf > rulegraph.pdf
snakemake --profile profiles/aws --forceall --filegraph | dot -Tpdf > filegraph.pdf
snakemake --profile profiles/aws/ all
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
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