Dinh/NOTES/2010-7-24

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Revision as of 22:51, 26 July 2010 by >Dinh
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BSPP Data from HL064

File Total #Mapped Total F&R % Mapped
s1 - BJiPS.DMR220K.txt.fwd.soap.out 19284556 8715423 15348294 0.795885266946255
s1 - BJiPS.DMR220K.txt.rev.soap.out 19284556 6632871
s3 - PGP1iPS.97K.txt.fwd.soap.out 18278561 6647739 13048545 0.713871567898589
s3 - PGP1iPS.97K.txt.rev.soap.out 18278561 6400806
s4 - PGP1fib.97K.txt.fwd.soap.out 14865064 4765887 9475863 0.637458607645416
s4 - PGP1fib.97K.txt.rev.soap.out 14865064 4709976
s5 - 01192B09.txt.fwd.soap.out 17014633 4497325 8909772 0.523653492849361
s5 - 01192B09.txt.rev.soap.out 17014633 4412447
s6 - 01373A17.txt.fwd.soap.out 17755423 6140866 11995320 0.675586270177849
s6 - 01373A17.txt.rev.soap.out 17755423 5854454
s7 - 01373B09.txt.fwd.soap.out 16901995 5794389 11360060 0.672113558192391
s7 - 01373B09.txt.rev.soap.out 16901995 5565671
s8 - 07292B09.txt.fwd.soap.out 18621718 7544808 15108002 0.81131085756964
s8 - 07292B09.txt.rev.soap.out 18621718 7563194
File CpG Covered >=10x Average Coverage
01192B09.txt.clean.soap.fwd.out.fwd.pileup.methylFreq.BED.txt 94313 33.2471027323911
01373A17.txt.clean.soap.fwd.out.fwd.pileup.methylFreq.BED.txt 90615 35.0399492357777
01373B09.txt.clean.soap.fwd.out.fwd.pileup.methylFreq.BED.txt 103324 34.6895106654795
07292B09.txt.clean.soap.fwd.out.fwd.pileup.methylFreq.BED.txt 99666 36.7683262095399
BJiPS.DMR220K.txt.clean.soap.fwd.out.fwd.pileup.methylFreq.BED.txt 12 11.3333333333333
PGP1fib.97K.txt.clean.soap.fwd.out.fwd.pileup.methylFreq.BED.txt 80301 33.4409285064943
PGP1iPS.97K.txt.clean.soap.fwd.out.fwd.pileup.methylFreq.BED.txt 141707 34.4084413614006
F & R Methyl Freq Correlation:
(B1) 01192B09-2: r^2=0.9453
(B3) 01373A17-2: r^2=0.9418
(B4) 01373B09-2: r^2=0.9535
(B14)07292B09-2: r^2=0.939
File:Hcorcluster-0 bc matrix.png
File:Hcorcluster-2 bc matrix.png

3_bc_matrix.txt

  1. Combine 01373A17 1 & 2
  2. Combine 01192B09
  3. Use 01373B09.2 and 07292B09.2