Noi/NOTES/2012-3-21: Difference between revisions

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=== Link to calendar: [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes]]===
= ASM analysis of UCLA SZ data set =
= ASM analysis of UCLA SZ data set =
* After discussing with Dr. Zhang and Dinh about how to identify sequence-dependent ASM, Dr. Zhang suggested to identify the consistency of sequence preference DNA methylation across individual
* After discussing with Dr. Zhang and Dinh about how to identify sequence-dependent ASM, Dr. Zhang suggested to identify the consistency of sequence preference DNA methylation across individual

Revision as of 18:07, 22 March 2012

Link to calendar: [[1]]

ASM analysis of UCLA SZ data set

  • After discussing with Dr. Zhang and Dinh about how to identify sequence-dependent ASM, Dr. Zhang suggested to identify the consistency of sequence preference DNA methylation across individual
  • After having more discussion with Dinh, she helped me out to write scripts for sequence-dependent ASM using binomial test and t-test by testing on ASM HAPMAP data (total 12 samples): [[2]]
on genome-miner: /home/nplongth/Noi_scratch/ASM_HAPMAP1362-1454_2012_02_03/DD_SequenceDependentTest
  • I did the same analysis on UCLA SZ data set
on genome-miner: /home/nplongth/Noi_scratch/ASM_UCLA/combined_ASM_UCLA-4batches_2012_01_24
  • Since there were mislabeling of some samples at the beginning from UCLA and after mapping and ASM analysis, and I generated many files. I still kept all labeling the same as original, but made the correction when generated the methylation matrix or other sample_list files for any analysis. Here are the list of samples used in analysis and correction.

Correct data mislabeling in UCLA.SZ data set
Note: --> = change the labeling to
GK0210-001 --> GK0210-002
GK0210-002 --> GK0210-001
GK0050-005a --> GK0277-002
GK0277-002 --> GK0344-004
GK0344-004 --> GK0050-005a

Binomial test

./asmBinomialTest.pl UCLA_MFASM_Qcpg_list.txt > UCLA_SZ_SeqDepTest_Binomial_PVal0.05.txt
  • I got total 8,510 SNP:CpG sites showing significant ASM using p-value cutoff 0.05. However, when I look closer to the fraction of methylation level, it showed that some significant sites by this test and p-value cutoff have very close methylation level or had the methylation fraction 0 on both alleles. I may try to increasing stringency by lowering the cufoff p-value and observe the resulting methylation fraction.
awk '{if ($98 <=0.01) print $0;}' UCLA_SZ_SeqDepTest_Binomial_PVal0.05.txt > UCLA_SZ_SeqDepTest_Binomial_PVal0.01.txt
  • After lowering p-val cutoff, I got total 4,708 SNP:CpG sites.
  • Note: 13:38445196:38445195 --> chromosome position: SNP position: CpG position

T-test

./asmTTest.pl UCLA_MFASM_Qcpg_list.txt > UCLA_SZ_SeqDepTest_TTest_PVal0.05.txt
  • I got total 9,123 SNP:CpG sites showing significant ASM using p-value cutoff 0.05.
awk '{if ($98 <=0.01) print $0;}' UCLA_SZ_SeqDepTest_TTest_PVal0.05.txt > UCLA_SZ_SeqDepTest_TTest_PVal0.01.txt
  • I got 8,281 SNP:CpG sites when using p-value cutoff 0.01
    • --> explain more
  • Extract number of significant ASM
    • SNP-free ASM:
    • SNP on CpG ASM:
./getnoSNPCpG.pl UCLA_SZ_SeqDepTest_Binomial_PVal0.01.txt > UCLA_SZ_SeqDep_Binomial-noSNP_PVal0.01.txt -->
./getSNPonCpG.pl UCLA_SZ_SeqDepTest_Binomial_PVal0.01.txt > UCLA_SZ_SeqDep_Binomial-SNPonCpG_PVal0.01.txt -->
./getnoSNPCpG.pl UCLA_SZ_SeqDepTest_Binomial_PVal0.05.txt > UCLA_SZ_SeqDep_Binomial-noSNP_PVal0.05.txt --> 
./getSNPonCpG.pl UCLA_SZ_SeqDepTest_Binomial_PVal0.05.txt > UCLA_SZ_SeqDep_Binomial-SNPonCpG_PVal0.05.txt --> 
./getnoSNPCpG.pl UCLA_SZ_SeqDepTest_TTest_PVal0.01.txt > UCLA_SZ_SeqDep_TTest-noSNP_PVal0.01.txt -->
./getSNPonCpG.pl UCLA_SZ_SeqDepTest_TTest_PVal0.01.txt > UCLA_SZ_SeqDep_TTest-SNPonCpG_PVal0.01.txt --> 
./getnoSNPCpG.pl UCLA_SZ_SeqDepTest_TTest_PVal0.05.txt > UCLA_SZ_SeqDep_TTest-noSNP_PVal0.05.txt -->
./getSNPonCpG.pl UCLA_SZ_SeqDepTest_TTest_PVal0.05.txt > UCLA_SZ_SeqDep_TTest-SNPonCpG_PVal0.05.txt -->
  • Comparing the the results from Binomial test an dTTest
    • p-value 0.01: there are 405 CpG site overlap: there are 38 site of SNP-free CpG and 366 SNP on CpG ASM
    • p-value 0.05: there are 623 CpG site overlap: there are 156 site of SNP-free CpG and 466 SNP on CpG ASM
./getnoSNPCpG.pl overlapped_UCLA_SZ_SeqDep_BinoTTest_PVal0.01.txt > overlapped_UCLA_SZ_SeqDep_BinoTTest-noSNP_PVal0.01.txt
./getSNPonCpG.pl overlapped_UCLA_SZ_SeqDep_BinoTTest_PVal0.01.txt > overlapped_UCLA_SZ_SeqDep_BinoTTest-SNPonCpG_PVal0.01.txt
./getnoSNPCpG.pl overlapped_UCLA_SZ_SeqDep_BinoTTest_PVal0.05.txt > overlapped_UCLA_SZ_SeqDep_BinoTTest-noSNP_PVal0.05.txt
./getSNPonCpG.pl overlapped_UCLA_SZ_SeqDep_BinoTTest_PVal0.05.txt > overlapped_UCLA_SZ_SeqDep_BinoTTest-SNPonCpG_PVal0.05.txt
  • --> describe more