Dinh/Dinh 2014/NOTES/2014-4-1
Jump to navigation
Jump to search
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