Noi/NOTES/2011-4-16

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  • Note: some pictures will be updated since need to remove the low quality samples

UPenn 48 African methylome samples data analysis[edit]

  • 48 sample list: Media:48SamplelistUPenn.xlsx
  • HiSeq data
    • Data is deconvoluted by Dr. Zhang
    • Sample sequences in different lanes were merged together, and 27 nt were trimmed from each read
    • SE mapping on Triton cluster (mapped to hg18/build36 version)
  • Data analysis plan by Dr. Zhang:
  • Number of reads, number of CpG count, % mapping: File:UPenn48sample BSPP data analysis.xlsx
  • Correlation coefficient (Dr. Zhang's script in /home/kunzhang/bin/frMethylCorr.pl and edited somepoint by Dinh): Media:frMethylCorr.xlsx
  • Minidepth =10

File:UPennhcorcluster-1scriptA.png

  • Then Dinh used another script to make another matrix file: details
    • /home/nplongth/UPenn48_220k_20110412/trimmed_SEMapped_MethylFreq/methyl.matrix.n48_10depth.txt

File:UPennhcorcluster-2B.png