Pipeline to download and preprocess TCGA transcriptome data.
nextflow run TCGA_pipeline.nf -c TCGA_pipeline.config
Modify "cancer_type" field of TCGA_pipeline.config file if you want to get data of other cancer type. Please refer to TCGA Study abbreviation (https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations) for available cancer types.
Gene length computed with GTF tools (https://www.genemine.org/gtftools.php) with the following code, which calculated gene length as a length of merged exons of isoforms (non-overlapping exonic length).
gtftools -l gencode.v36.geneLength.exon_length gencode.v36.annotation.gtf