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Bioinformatics. 2012 Feb 15;28(4):587-8. doi: 10.1093/bioinformatics/btr699. Epub 2011 Dec 22.

MeQA: a pipeline for MeDIP-seq data quality assessment and analysis.

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  • 1School of life science, Tongji University, 200092 Shanghai, China. jhuang@cephb.fr



We present a pipeline for the pre-processing, quality assessment, read distribution and methylation estimation for methylated DNA immunoprecipitation (MeDIP)-sequence datasets. This is the first MeDIP-seq-specific analytic pipeline that starts at the output of the sequencers. This pipeline will reduce the data analysis load on staff and allows the easy and straightforward analysis of sequencing data for DNA methylation. The pipeline integrates customized scripting and several existing tools, which can deal with both paired and single end data.


The package and extensive documentation, and comparison to public data is available at http://life.tongji.edu.cn/meqa/.

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