Journal of Animal Science and Biotechnology

Table 2 Analyze software models

From: Whole-genome methylation analysis reveals epigenetic variation between wild-type and nontransgenic cloned, ASMT transgenic cloned dairy goats generated by the somatic cell nuclear transfer

Analysis	Software or database	Version
Data QC	Cutadapt [22]	Version 1.9.1
Mapping	Bismark [23]	Version 0.7.12
Differeantial mCpG sites	MethylKit [24]	Version 3 0.7.12
Detection and annotaion	Samtools [25]	Version1.6
Detection and annotaion	Annovar [26]	Version 21 Feb 2013
DMR	swDMR [27]	Version 1.0.7
DMR	Annovar [26]	Version 21 Feb 2013
Enrichment analysis	GO Database [28, 29]
Enrichment analysis	KEGG Database [30, 31]	Version 03/21/2011

addresses
• GO DataBase: http://geneontology.org/
• KEGG DataBase: http://www.genome.jp/kegg/kegg1.html
• Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
• MethylKit: https://github.com/al2na/methylKit
• swDMR: https://sourceforge.net/projects/swdmr/

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ISSN: 2049-1891

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