Kun:LabNotes/MONOD/2015-1-14
Jump to navigation
Jump to search
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.