A study on open chromatin based on pair-end sequencing data

Abstract

Open chromatin regions are important for understanding gene regulation mechanism. Due to the recent development of ATAC-seq, it is possible to determine open chromatin regions for clinical samples with as little as 500 cells. Existing peak-calling methods predict peaks from the signal profile formed by piling up the sequencing tags. These methods do not utilize the paired-end information of the sequencing tags. This thesis proposes a new peak caller OpenEM that uses this additional feature to achieve better peak-calling performance. In addition, it also proposes a new scoring scheme for transcription start sites called OpenTSS.