Melanoma_Progression_Gene_Analysis

RNA sequencing processing and read count quantification:

1. FastQC quality control:
   • program: fastqc.snakefile.py
2. Trimming and repeat FastQC:
   • program: fastqc_trimmomatic.snakefile.py
3. Read mapping to a sex-specific reference genome and read count quantification with salmon:
   • program: salmon.snakefile

• All programs run in a conda environment for version control. Conda environment can be recreated with fastqc_environment.yml

• Sex-specific reference genomes created with the GENCODE GRCH38 genome by hard masking the y-chromosome for the female-specific reference genome and hard masking the pseudoautosomal regions of the y-chromosome for the male-specific genome

Data analysis:

1. Differential expression analysis, visualization, and regularized regression models:
   • program: Differential_Expression_Krueger_Bastian_Scatolini.Rmd
2. Association of genes with progression of melanoma
   • program: Scatolini_progression_of_genes.Rmd

• Gene lists were harmonized using David Web Services to convert all probe names from the Krueger and Scatolini datasets into official gene symbols