Scripts for figures and results in LocusMasterTE paper
Rscripts used to generate main figures.
Containing supplementary information about data used.
- Used_SG-Nex_accession_list.xlsx: Excel file contains information about used samples in SG-NEx study with sample ID.
- Processed_long_read.xlsx: Links directed to "processed long-read TPM counts" readily used as long-read input in LocusMasterTE.
6 samples with 5 different cell lines. Two HCT116 samples exist generated from our lab and SG-NEx study.
Important commands use to preprocess samples. Largely contains three major parts.
- Processing long-read: Minimap2 and FeatureCounts
- Aligning short-read: STAR
- Simulation commands: Spanki