Protocols

BiQ Analyzer HiMod specifications

Information


Unique identifier OMICS_04129
Name BiQ Analyzer HiMod
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for BiQ Analyzer HiMod

BiQ Analyzer HiMod citations

 (2)
library_books

Comprehensive Evaluation of Commercial Bisulfite Based DNA Methylation Kits and Development of an Alternative Protocol With Improved Conversion Performance

2018
PMCID: 5888801
PMID: 29636635
DOI: 10.1177/1179237X18766097

[…] feld, Germany), diluted, pooled, and sequenced (Illumina v3 chemistry, 2 × 300 bp paired end) on Illumina MiSeq following the manufacturer’s instructions. Alignments and evaluation were done with the BiQ Analyzer HiMod program filtering all reads with more than 10% unrecognized CpG sites.A detailed protocol for OPTI-Bisulfite is provided in Supplementary File 1. Briefly, 94 µL bisulfite solution ( […]

call_split

The tobacco carcinogen NNK drives accumulation of DNMT1 at the GR promoter thereby reducing GR expression in untransformed lung fibroblasts

2018
Sci Rep
PMCID: 5861118
PMID: 29559689
DOI: 10.1038/s41598-018-23309-2
call_split See protocol

[…] it (QIAGEN, UK). The DNA samples were sent to Inqaba Biotec for sequencing using the MiSeq v3 platform (Illumina®).Quality control on the data was performed using Galaxy software (version 15.10.dev). BiQ Analyzer HiMod (Becker et al.) was then used to determine the methylation levels of the amplified promoters in each treatment relative to the 72 h vehicle-treated cells. […]

BiQ Analyzer HiMod institution(s)
Department of Genetics, Saarland University, Saarbrücken, Germany Department of Computational Biology and Applied Algorithms, Max-Planck Institute for Informatics, Saarbrücken, Germany; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria

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