BiQ Analyzer HT protocols

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BiQ Analyzer HT statistics

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BiQ Analyzer HT specifications

Information


Unique identifier OMICS_00631
Name BiQ Analyzer HT
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for BiQ Analyzer HT

BiQ Analyzer HT in pipeline

2016
PMCID: 4999891
PMID: 27561320
DOI: 10.1038/srep32187

[…] bowtie 2  using gene sequences in silico bisulfite converted as a reference. alignment bam files were then sorted by target and condition using bamtools split function. sorted reads were analyzed in biq analyzer ht setting parameters at 100% of the read length, 90% sequence identity, bisulfite conversion efficiency ≥98% and lower cutoff at 30 reads per cpg site analyzed. the methylation level […]


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BiQ Analyzer HT in publications

 (8)
PMCID: 5808295
PMID: 29467769
DOI: 10.3389/fimmu.2018.00199

[…] germany) according to manufacturer’s instructions and sequenced on the illumina miseq platform using miseq reagent kit v3 (illumina, inc., san diego, usa). sequencing results were processed with biq analyzer ht () and filtered according to sequence identity (>0.9), bisulfite conversion (>0.95), and fraction of unrecognized sites (<0.1). data for methylation of the indicated regions […]

PMCID: 5692129
PMID: 29162979
DOI: 10.1177/1179237X17736107

[…] chip 314 as previously described., bam files, the output data from amplicon sequencing, were converted to fasta format by bam tools (https://usegalaxy.org/). the converted data were loaded into biq analyzer ht (http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/) and minimal conversion rates set at 1.0. from the results, the mean methylation levels of each sample, methylation profile […]

PMCID: 4924566
PMID: 27366675
DOI: 10.1016/j.mex.2015.11.008

[…] sorted with the primer sequences for each pcr product using a custom perl script (). finally, the sorted sequences for each pcr product are used for calculating its dna methylation levels with biq analyzer ht . a set of additional perl scripts have been prepared to execute the process of biq analyzer ht on a batch mode ()., , , 1. combine all the pcr products […]

PMCID: 4678850
PMID: 26338779
DOI: 10.1093/nar/gkv867

[…] remaining sequences were sorted to an initial pcr product based on its two primer sequences. the sorted sequences for each locus were used for calculating dna methylation levels for each locus using biq analyzer ht tool (). the bioinformatic pipeline used for this process is available upon request., in the current study, tcga (the cancer genome atlas) database was used to survey the expression […]

PMCID: 4278373
PMID: 25554740
DOI: 10.1016/j.gdata.2014.11.013

[…] chips (ion torrent, life technologies)., we have implemented the following bioinformatics pipeline to process the raw sequence reads from the ngs platform (). we have used bowtie2 for mapping and biq analyzer ht for dna methylation analyses. we have used several unix-based command lines along with custom-made perl scripts for the pipeline. first, we used the following steps […]


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BiQ Analyzer HT institution(s)
Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany

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