/bulk-gene-counts-HGSOC

Scripts for bulk RNA-seq gene count tables for HGSOC project

Primary LanguageShellMIT LicenseMIT

bulk-gene-counts-HGSOC

Scripts to process bulk RNA-seq samples in HGSOC project.

Scripts to run in order are:

  • salmon_index.sh - generate transcriptome index for Salmon
  • salmon_quantify.sh - quantify RNA-seq reads at transcript level using Salmon
  • gene_counts_tximeta.R - import transcript counts and aggregate to gene counts using tximeta

Sample names

Note that bulk and single-cell RNA-seq sample names in this dataset are in a different order:

bulk sample name single-cell sample name
17667X1 16030X3
17667X2 16030X2
17667X3 16030X4