BSeQC pipeline

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


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  • person_outline Wei Li <>

Publication for BSeQC

BSeQC IN pipeline

PMCID: 4790440
PMID: 26366945
DOI: 10.2217/epi.15.21

[…] can bias a methylation estimate at these positions. this issue can be addressed by a standalone program trim galore [43] or handled automatically in the later version of saap-rrbs [44]. the tool, bseqc [45], can also be used, which takes aligned sam/bam and generates a new file with the incorporated bases removed., the qc steps for dna illumina microarray have been described previously, […]

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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