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BSeQC

A package to comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases that may result in inaccurate methylation estimation. BSeQC takes standard SAM/BAM files as input and generates bias-free SAM/BAM files for downstream analysis. Evaluation based on real BS-seq data indicates that the use of the bias-free SAM/BAM file substantially improves the quantification of methylation level.

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BSeQC forum

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BSeQC classification

BSeQC specifications

Software type:
Package/Module
Restrictions to use:
None
Output format:
SAM, BAM, PDF, text
Programming languages:
Python
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Input format:
SAM, BAM
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Stability:
Stable

BSeQC distribution

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No versioning.

BSeQC support

Documentation

Maintainer

  • Wei Li <>

Credits

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Publications

Institution(s)

Department of Bioinformatics, School of Life sciences and Technology, Tongji University, Shanghai, China; Dan L Duncan Cancer Center; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA

Funding source(s)

973 Program of China [2010CB944900], CPRIT RP110471-C3 and NIH [R01HG007538]

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