This README file provides information on Mate-pair sequencing experiments performed on Control, Step 1, and Step 2 neurons from CK-p25 mice induced for 2 weeks.

Mate-pair Sequencing
The R scripts used for processing Mate-pair sequencing data are located in the Mate-Pair-seq/ folder.

Mate-pair Sequencing R Scripts
1. MatePair_mapping.R
2. MatePair_BedstoPairefiles.R
3. MatePair_distancePlots.R

Processing Steps:
1. The R script MatePair_mapping.R takes paired-end mate-pair sequencing reads (GEOGSE227445), maps each paired read separately to the genome, and creates corresponding bed files.
2. The R script MatePair_BedstoPairefiles.R merges the paired bed files to create mate-pair files.
3. The R script MatePair_distancePlots.R creates a histogram of mapped read pair distances.