Kun:LabNotes/MONOD/2015-1-14

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Integrative analysis of RRBS, WGBS/LC, WGBS/BSPP data[edit]

  • With all the data generated in the past six months, it's time to start combining all the data for an integrative analysis.
  • Here is the overall strategy:
    • Generate hapInfo file from each bam file (use the latest Jan2015 scripts, which derive the consensus haplotypes from multiple clonal reads based on read quality).
    • Identify informative regions based on the primary tumor and normal plasma data. Do this for RRBS and WGBS/LC separately, then merge the regions.
    • Generate another batch of hapInfo files for these informative regions only.
    • Run mixMethHapAnalysis and also determine tumor HMH load in patient plasma samples.