Dinh 2011/NOTES/2011-12-21

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Re-subsetting DMR220k (w/o Exp1-3)

  • Many of the library-free samples have been captured with normalization (subsetting and suppressor oligos), hence I was able to evaluate just the performance of the probes within each subset and could not compare across subsets.
    • I obtained a list of probes which never captured across multiple experiments.
http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-12-8
    • I need to double check that the never performing probes were not the ones we have designed suppressor oligos for.
  • We have samples captured without normalization but the libraries were generated using the N2-adapter protocol, which I found have lower specificities (fewer reads mapping to target probes region)
  • I decided to go back to the library-free data from BJiPS captured for the rebalancing experiment
http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/NOTES/2010-9-23
    • Indx1-7 were captured with the individual subsets, however, the amount of probes to target were all the same.
    • I will be able to compare the performance of probes across subsets and thereby be able to re-subset the probes.
  • I re-mapped the data with 27 bp trimmed from 3 prime end. I also used a more precise protocol to map reads to probes
http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-1