BiQ Analyzer HT statistics

info info

Citations per year

info

Popular tool citations

chevron_left DNA methylation visualization Read alignment chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

Protocols

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

Versioning


No version available

Publication for BiQ Analyzer HT

BiQ Analyzer HT citations

 (9)
library_books

CD137+CD154− Expression As a Regulatory T Cell (Treg) Specific Activation Signature for Identification and Sorting of Stable Human Tregs from In Vitro Expansion Cultures

2018
Front Immunol
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 […]

library_books

Association of Tissue Specific DNA Methylation Alterations with α Thalassemia Southeast Asian Deletion

2017
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 […]

call_split

Remodelling of the hepatic epigenetic landscape of glucose intolerant rainbow trout (Oncorhynchus mykiss) by nutritional status and dietary carbohydrates

2016
Sci Rep
PMCID: 4999891
PMID: 27561320
DOI: 10.1038/srep32187
call_split See protocol

[…] 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 […]

library_books

NGS based deep bisulfite sequencing

2015
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 […]

library_books

Epigenetic instability of imprinted genes in human cancers

2015
Nucleic Acids Res
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 […]

library_books

Locus specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High Throughput Targeted Repeat Element Bisulfite Sequencing

2014
Genom Data
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 […]


Want to access the full list of citations?
BiQ Analyzer HT institution(s)
Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany

BiQ Analyzer HT reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review BiQ Analyzer HT