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BSeQC specifications


Unique identifier OMICS_00572
Name BSeQC
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM, BAM
Output format SAM, BAM, PDF, text
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Wei Li

Publication for BSeQC

BSeQC citations


Decoding the dynamic DNA methylation and hydroxymethylation landscapes in endodermal lineage intermediates during pancreatic differentiation of hESC

Nucleic Acids Res
PMCID: 5888657
PMID: 29394393
DOI: 10.1093/nar/gky063

[…] paired mode and two allowable mismatches. in total, we identified 14.6 million cpg sites with coverage ≥10 reads and our downstream bioinformatic analyses were based on these cpg sites. moabs () and bseqc () were used to do the quality control and to calculate the methylation ratio for each cpg site. we defined dmrs as the regions between two samples that have an absolute difference of mean dna […]


Sparse conserved under methylated CpGs are associated with high order chromatin structure

Genome Biol
PMCID: 5580327
PMID: 28859663
DOI: 10.1186/s13059-017-1296-x

[…] wgbs sample in 31 normal cell types (additional file : table s5), we use bsmap to trim adaptor and low-quality sequences with default threshold, align bisulfite-treated reads to human hg19 genome. bseqc [] was then used to remove the technical biases in wgbs data, introduced by end repair, polymerase chain reaction (pcr) amplification, and overlapping segments in paired-end reads. we used […]


Tet2 and Tet3 cooperate with B lineage transcription factors to regulate DNA modification and chromatin accessibility

PMCID: 5142813
PMID: 27869616
DOI: 10.7554/eLife.18290.030

[…] based on cytosine methylation in non-cpg context. for all the samples the bisulfite conversion efficiency was higher than 0.9936. duplicated reads caused by pcr amplification were removed by bseqc v1.2.0 () applying a poisson p-value cutoff of 1e-5. consequently, a maximum of three stacked reads at the same genomic location were allowed and kept for further analysis. in addition, bseqc […]


Large conserved domains of low DNA methylation maintained by Dnmt3a

Nat Genet
PMCID: 3920905
PMID: 24270360
DOI: 10.1038/ng.2836

[…] a read can be mapped to multiple locations with the same fewest mismatches, this read is determined as a multi-mapped read and its mapping location was randomly selected from all mapping locations., bseqc was used to remove technical biases in wgbs data. first, we removed clonal reads with identical sequences resulting from possible over-amplification during sample preparation. these clonal […]

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BSeQC 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
BSeQC funding source(s)
973 Program of China [2010CB944900], CPRIT RP110471-C3 and NIH [R01HG007538]

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