Transcriptionally Active Regions are regions of the genome (including all introns, exons, and non-coding elements of the genome) which get transcribed into mRNA. Single cell sequencing technology has enabled detection of these transcripts at a cellular level, which has opened up the huge potential to study cell-type specific coding and non-coding elements in the genome.
This repository contains code for generating a counts matrix for non-coding elements from 10x single cell sequencing BAM files, which is a specially challenging problem due to lack of an annotation file for alignment.