RRBS-Analyser: A Comprehensive Web Server for Reduced Representation Bisulfite Sequencing Data Analysis

2013 ◽  
Vol 34 (12) ◽  
pp. 1606-1610 ◽  
Author(s):  
Tao Wang ◽  
Qi Liu ◽  
Xianfeng Li ◽  
Xiaobing Wang ◽  
Jinchen Li ◽  
...  
Keyword(s):  
Data Analysis ◽  
Bisulfite Sequencing ◽  
Web Server ◽  
Sequencing Data ◽  
Reduced Representation ◽  
Reduced Representation Bisulfite Sequencing ◽  
Bisulfite Sequencing Data ◽  
Sequencing Data Analysis

scholarly journals WBSA: Web Service for Bisulfite Sequencing Data Analysis

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e86707 ◽  
Author(s):  
Fang Liang ◽  
Bixia Tang ◽  
Yanqing Wang ◽  
Jianfeng Wang ◽  
Caixia Yu ◽  
...  
Keyword(s):  
Data Analysis ◽  
Web Service ◽  
Bisulfite Sequencing ◽  
Sequencing Data ◽  
Bisulfite Sequencing Data ◽  
Sequencing Data Analysis

scholarly journals LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis

2018 ◽  
Author(s):  
Maia Malonzo ◽  
Viivi Halla-aho ◽  
Mikko Konki ◽  
Riikka J. Lund ◽  
Harri Lähdesmäki
Keyword(s):  
Dna Methylation ◽  
Data Analysis ◽  
Bisulfite Sequencing ◽  
Bisulfite Conversion ◽  
Sequencing Data ◽  
Dna Libraries ◽  
Conversion Rates ◽  
Bisulfite Sequencing Data ◽  
Low Efficiency ◽  
Sequencing Data Analysis

AbstractDNA methylation is measured using bisulfite sequencing (BS-seq). Bisulfite conversion can have low efficiency and a DNA sample is then processed multiple times generating DNA libraries with different bisulfite conversion rates. Libraries with low conversion rates are excluded from analysis resulting in reduced coverage and increased costs. We present a method and software, LuxRep, that accounts for technical replicates from different bisulfite-converted DNA libraries. We show that including replicates with low bisulfite conversion rates generates more accurate estimates of methylation levels and differentially methylated sites.AvailabilityAn implementation of the method is available at https://github.com/tare/LuxGLM/tree/master/[email protected]

scholarly journals Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Aniruddha Chatterjee ◽  
Euan J. Rodger ◽  
Peter A. Stockwell ◽  
Robert J. Weeks ◽  
Ian M. Morison
Keyword(s):  
Bisulfite Sequencing ◽  
Flow Cell ◽  
Throughput Capacity ◽  
Sequencing Data ◽  
Bioinformatics Pipeline ◽  
Illumina Hiseq ◽  
Reduced Representation ◽  
Reduced Representation Bisulfite Sequencing ◽  
Unique Mapping ◽  
Nucleotide Resolution

Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform have not been previously described. We have made modifications to the RRBS library preparation protocol to sequence multiplexed libraries on a single flow cell lane of the Illumina HiSeq 2000. Furthermore, our analysis incorporates a bioinformatics pipeline specifically designed to process bisulfite-converted sequencing reads and evaluate the output and quality of the sequencing data generated from the multiplexed libraries. We obtained an average of 42 million paired-end reads per sample for each flow-cell lane, with a high unique mapping efficiency to the reference human genome. Here we provide a roadmap of modifications, strategies, and trouble shooting approaches we implemented to optimize sequencing of multiplexed libraries on an a RRBS background.

scholarly journals deepTools2: a next generation web server for deep-sequencing data analysis

2016 ◽  
Vol 44 (W1) ◽  
pp. W160-W165 ◽  
Author(s):  
Fidel Ramírez ◽  
Devon P Ryan ◽  
Björn Grüning ◽  
Vivek Bhardwaj ◽  
Fabian Kilpert ◽  
...  
Keyword(s):  
Data Analysis ◽  
Deep Sequencing ◽  
Web Server ◽  
Next Generation ◽  
Sequencing Data ◽  
Deep Sequencing Data ◽  
Sequencing Data Analysis
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