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Pipeline publication

[…] ere as follow: a minimum coverage of 10× in all replicates, a minimum of 25% of methylation difference between conditions with a corresponding adjusted P value (FDR) of 0.01. Methylkit defines methylation difference as absolute value of methylation percentage change between test and control. Since there is no data in oyster about the degree of methylation change that is necessary to obtain a biological impact we tentatively used the 25% default value. MethylExtract 1.8.1 [] was used to generate Methylation 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 with DeepTools [] on the public Galaxy instance (https://usegalaxy.org/). We used our earlier produced RNA-Seq based annotation of the genome []. Correlation analysis between DNA methylation and gene expression was performed using the Pearson and Apos correlation tool under the public galaxy instance (https://usegalaxy.org/). Average HTSeq count per gene [] was used for the gene expression level. Average DNA methylation profile per gene for the three biological replicates was generated. The fold change in expression observed between the diuron and seawater control conditions was the result of the DESeq analysis []. The fold change in DNA methylation between the diuron and seawater control conditi […]

Pipeline specifications

Software tools MethylExtract, VCFtools, deepTools