Scripts to process bulk RNA-seq samples in HGSOC project.
Scripts to run in order are:
salmon_index.sh
- generate transcriptome index for Salmonsalmon_quantify.sh
- quantify RNA-seq reads at transcript level using Salmongene_counts_tximeta.R
- import transcript counts and aggregate to gene counts using tximeta
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 |