Abstract: The primary tool currently used to pre-process 10X chromium single-cell ATAC-seq data is Cell Ranger, which can take very long to run on standard datasets. To facilitate rapid pre-processing that enables reproducible workflows, we present a suite of tools called scATAK for pre-processing single-cell ATAC-seq data that is 15 to 18 times faster than Cell Ranger on mouse and human samples. Our tool can also calculate chromatin interaction potential matrices and generate open chromatin signal and interaction traces for cell groups. We use scATAK tool to explore the chromatin regulatory landscape of a healthy adult human brain and unveil cell-type specific features, and show that it provides a convenient and computational efficient approach for pre-processing single-cell ATAC-seq data.
Abstract: Leptospirosis occurs worldwide (except the
poles of the earth), urban and rural areas, developed and
developing countries, especially in Thailand. It can be
transmitted to the human by rats through direct and indirect
ways. Human can be infected by either touching the infected rats
or contacting with water, soil containing urine from the infected
rats through skin, eyes and nose. The data of the people who
are infected with this disease indicates that most of the
patients are adults. The transmission of this disease is studied
through mathematical model. The population is separated into human
and rat. The human is divided into two classes, namely juvenile
and adult. The model equation is constructed for each class. The
standard dynamical modeling method is then used for
analyzing the behaviours of solutions. In addition, the
conditions of the parameters for the disease free and endemic
states are obtained. Numerical solutions are shown to support the
theoretical predictions. The results of this study guide the way to
decrease the disease outbreak.