Codes related to the NSV paper
#Fig3_TSS_CHIP: This folder included codes to analyze integration sites. We first analyzed the relationship between integration sites and transcription start site (TSS) using nearestTSS function from edgeR package. We then tried to verify the results using another database (refTSS_v3.1_human_coordinate.hg38). Then we look at the relationship between integration sites and histone marks using a publically available database (Roadmap). Please download the following files into the CHIP folder
https://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/narrowPeak/
~E043-H3K4me1.narrowPeak.gz ~E043-H3K4me3.narrowPeak.gz ~E043-H3K9me3.narrowPeak.gz ~E043-H3K27ac.narrowPeak.gz ~E043-H3K27me3.narrowPeak.gz ~E043-H3K36me3.narrowPeak.gz
#Fig4_RNASeq: This folder contained code analyzing RNA-Seq data. Raw count expression matrices from control and NSV groups were included.