Lecture 9

Set up directory and copy over files

Check out the first few lines from GSC.chr3.meth

head GSC.chr3.meth

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Set up variables

export PATH=/home/hgen_share/utils/bin:$PATH

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Calculate differential methylation with methdiff

dnmtools diff -o chr3.methdiff EpiLC.chr3.meth GSC.chr3.meth

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Identify HMRs with hmr Do the same for EpiLC

dnmtools hmr -o GSC.chr3.hmr GSC.chr3.meth

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Call DMRs usign dmr

dnmtools dmr chr3.methdiff EpiLC.chr3.hmr GSC.chr3.hmr DMR_EpiLC_lt_GSC.bed DMR_GSC_lt_EpiLC.bed

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Determine PMDs with pmd Do the same for EpiLC

dnmtools pmd -o GSC.chr3.pmd.bed GSC.chr3.meth

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Add a .bed extension to the .hmr files. Download .bw & .bed result files to your local computer

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