Dinh/Dinh 2014/NOTES/2014-4-1

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DMR finding with MOdel-based Analysis of Bisulfite Sequencing data (MOABS)

  • Using only the mcomp module from the MOABS pipeline requires:
 1. setting LC_ALL variable with:
    export LC_ALL=C
 2. installing RInside for R. Open R and type:
    install.packages("RInside")
  • The input for mcomp is a G.bed file (ie), more detailed explanation see the MOABS documentations.
 #chrom	start	end	ratio	totalC	methC	strand	next	Plus	tcP	mcP	Minus	tcM	mcM
 chr5	3009585	3009587	1	1	1	-	G	+	0	0	-	1	1
 chr5	3011471	3011473	0.711	45	32	B	G	+	28	18	-	17	14

Analysis of mouse WGBS

  • Prepare the G.bed files with methylFreq2Gbed.pl (genome-miner)
 /home/dinh/scripts/methylFreq2GBED.pl 1 < [methylFreq] > [BED name]
  • We perform 3 tests:
 esc versus ipsc
 esc versus scnt
 ipsc versus scnt