Snakemake workflow

Title: Extracting HERV Expression in Cutaneous Melanoma Datasets

Bulk RNA-Seq Telescope analysis of TCGA-SKCM cutaneous melanoma samples (restricted access). Input the metadata table that include the accessions needed to download the raw sequencing files, output gene/HERV count matrices.

Dataset Citations

Watson, I. R., Wu, C. J., Zou, L., Gershenwald, J. E., Chin, L., & Melanoma Analysis Working Group and The Cancer Genome Analysis Research Network. (2015). Genomic classification of cutaneous melanoma. Cancer Research, 75(15_Supplement), 2972-2972.

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 curl to download files.

Usage

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/TCGA_SKCM_mets