Scripts used for Xist-mediated chromosome silencing analysis
- Mapping the Fastq reads into N-masked genome, where SNPs were masked by"N", with RunSTAR_mm10.sh
- Split the alignment into allelic bamfile with Split.sh
- Count the reads number for each gene with HTseq
- Normalisation and making expression table with python AllelicAnalysis.py configure.file
- Calculating the Repression Score with CalculateSilencing.R
- Permutation and Calculate the significance with Analysis_Permutaion.R