This README file provides information on Break Labelling In-Situ and Sequencing (BLISS) experiments performed on Control, Step 1, and Step 2 neurons from CK-p25 mice induced for 2 weeks.

Break Labelling In-Situ and Sequencing (BLISS)
BLISS was performed on Control, Step 1, and Step 2 neurons from CK-p25 mice induced for 2 weeks. The R scripts used for processing are located in the BLISS/ folder.

BLISS R Scripts
1. BLISS_Rscript_removePCRdupsUMIs_Replicat1.R
2. BLISS_Rscript_removePCRdupsUMIs_Replicat2.R
3. BLISS_Rscript_Mappingafterdedup.R

Processing Steps:
1. The R scripts BLISS_Rscript_removePCRdupsUMIs_Replicat1.R and BLISS_Rscript_removePCRdupsUMIs_Replicat2.R take the parsed single-end BLISS fastq files (GEOGSE227445) and remove PCR duplicates based on reads having identical Unique Molecular Identifiers (UMI).
2. The R script BLISS_Rscript_Mappingafterdedup.R maps the PCR duplicate removed fastq files and creates bed files for DNA double-strand break locations.