LocusMasterTE_paper

Scripts for figures and results in LocusMasterTE paper

Figures_Rscripts

Rscripts used to generate main figures.

Data_lists

Containing supplementary information about data used.

1. Used_SG-Nex_accession_list.xlsx: Excel file contains information about used samples in SG-NEx study with sample ID.
2. 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.

preprocessing_commands.sh

Important commands use to preprocess samples. Largely contains three major parts.

1. Processing long-read: Minimap2 and FeatureCounts
2. Aligning short-read: STAR
3. Simulation commands: Spanki