A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing
Year: 2015
Type: article
Abstract: Summary: Currently available bisulfite sequencing tools frequently suffer from low mapping rates and low methylation calls, especially for data generated from the Illumina sequencer, NextSeq. Here, we introduce a sequential trimming-and-retrieving alignment approach for investigating DNA methylation patterns, which significantly improves the number of mapped reads and covered CpG sites. The method is implemented in an automated analysis toolkit for processing bisulfite sequencing reads. Availability and implementation: http://mysbfiles.stonybrook.edu/~xuefenwang/software.html and https://github.com/xfwang/BStools. Contact: [email protected] Supplementary information: Supplementary materials are available at Bioinformatics online.
Source: Bioinformatics
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Awards: G1625195244, G1755495520, G239884891, G3583515671, G444632500, G479850928, 1/2: Partnership to study racial/ethnic differences in GI cancer biology, COMPUTATIONAL AND FUNCTIONAL APPROACHES TO VALIDATING CANCER GENOME TARGETS, G7721780970, Host-environment interactions in the pathophysiology of digestive disease, Cancer Center Support Grant, CSHL Cancer Center Support Grant
OpenAlex ID: W2164408734