MethylExtract protocols

View MethylExtract computational protocol

MethylExtract statistics

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MethylExtract specifications

Information


Unique identifier OMICS_00605
Name MethylExtract
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.8.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Michael Hackenberg <>

Publication for MethylExtract

MethylExtract in pipeline

2017
PMCID: 5804544
PMID: 29492306
DOI: 10.1093/eep/dvx004

[…] wiggle and bed files that were displayed in igv [] for visual inspection of the data genomic regions (promoter, exon, intron or intergenic region) affected by parental exposure to diuron. methylextract served also to generate genetic variant calls in vcf format. vcf files were analyzed with vcftools v0.1.12b []. average methylation profiles over transcribed regions were generated […]


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MethylExtract in publication

PMCID: 5804544
PMID: 29492306
DOI: 10.1093/eep/dvx004

[…] and the observed dna methylation (epiallele frequency) differences could be an expression of such underlying genetic (allele frequency [af]) difference. we used the genetic variants obtained with methylextract to search for signs of selection on a genome wide level. we used a total of 11 425 759 snps (control) and 9 517 133 snps (diuron) to calculate tajima’s d in 200 kb sliding windows. […]


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MethylExtract institution(s)
Dpto de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain; Lab de Bioinformática, Inst de Biotecnología, Centro de Investigación Biomédica, Granada, Spain

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