MethyQA specifications


Unique identifier OMICS_04218
Name MethyQA
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output format Tab-delimited text
Operating system Unix/Linux
Programming languages Perl, Python, R
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Shuying Sun

Publication for MethyQA

MethyQA citations


HMPL: A Pipeline for Identifying Hemimethylation Patterns by Comparing Two Samples

Cancer Inform
PMCID: 4530977
PMID: 26308520
DOI: 10.4137/CIN.S17286

[…] cing data. If users find some serious sequencing quality issues in their data, we recommend that they check data more thoroughly using other available software packages, such as SAAP-RRBS, BSeQC, and MethyQA, before they interpret their HMPL results. […]


Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis

PMCID: 4790440
PMID: 26366945
DOI: 10.2217/epi.15.21
call_split See protocol

[…] methylation occurs), which is generally greater than 99.5%. These QC steps are integrated as part of analytical pipeline of SAAP-RRBS (or SAAP-BS) []. Specialized QC tools are also available such as MethyQA and BSeQC [,].Additional QC is necessary before jumping into correlative analysis with phenotypical data. CpGs with low coverage (<10× for example) should be excluded. After multiple samples a […]

MethyQA institution(s)
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA; Department of Mathematics, Texas State University, San Marcos, TX, USA; Department of Electrical Engineering and Computer Sciences, Case Western Reserve University, Cleveland, OH, USA

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