BSPAT

[…] (> q30) and for read lengths (> 100 bp) and converted into fasta format in a galaxy project environment []. to evaluate the methylation ratio of each cpg, we loaded fasta files into the bisulfite sequencing pattern analysis tool (bspat—http://cbc.case.edu/bspat/index.jsp) []. in parallel, we used perl to create single specific files for every interrogated gene, […]

[…] bisulfite-treated reads analysis tool (burrows–wheeler transform), ucsc genome browser university of california santa cruz genome browser, wbsa web service for bisulfite sequencing data analysis, bspat bisulfite sequencing pattern analysis tool, gbsa genome bisulfite sequencing analyser, igv integrative genomics viewer, saap-rrbs streamlined analysis and annotation pipeline for rrbs data, […]

[…] our dataset., convolution prior was adopted for φ[i] and ν[j,i] [], denoting they both may be decomposed into the sum of unstructured (e.g. ush, ssh) and spatial structured random effects (e.g. bind, bspat):7\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \use […]

[…] (x1, x2) refers to the coordinates of the location of the data point, latitude and longitude, or location centroids based on the map. the prior for bspat, ij = (bspat,11, bspat,12, …, bspat,kk) is based on spatial smoothness priors common in spatial statistics (see []). the most commonly used prior specification based on the four nearest […]