Chromosomal Instability Estimation Based on Next Generation Sequencing and Single Cell Genome Wide Copy Number Variation Analysis
Fig 1
Epic Sciences single cell NGS-based CNV analysis pipeline.
FASTQ files were aligned to hg38 human reference genome from UCSC using BWA. BAM files with a MAPQ quality score greater than 30 were kept for further analysis with two separate pipelines: analysis pipeline 1 for genomic instabilities estimation using 1M bp window; analysis pipeline 2 for determining copy number alterations of individual genes.