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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 probe, which eliminated much of the overlapping probes issue. (Note: DMR220K seems to have a lot of overlapping probes.) http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh_2011/NOTES/2011-11-1 {| {{table}} border=1 | align="center" style="background:#f0f0f0;"|'''Dataset''' | align="center" style="background:#f0f0f0;"|'''Indx1 (Sub1 capture)''' | align="center" style="background:#f0f0f0;"|'''Indx2 (Sub2 capture)''' | align="center" style="background:#f0f0f0;"|'''Indx3 (Sub3 capture)''' | align="center" style="background:#f0f0f0;"|'''Indx4 (Sub4 capture)''' | align="center" style="background:#f0f0f0;"|'''Indx5 (Sub5 capture)''' | align="center" style="background:#f0f0f0;"|'''Indx6 (Sub6 capture)''' | align="center" style="background:#f0f0f0;"|'''Indx7 (Sub7 capture)''' |- | '''Sub1''' (total reads count)||291276||34||249||168||130||44||60 |- | '''Sub2''' (total reads count)||20||345936||156||169||141||26||374 |- | '''Sub3''' (total reads count)||207||124||2462052||3181||1616||437||327 |- | '''Sub4''' (total reads count)||87||67||1398||2108636||609||168||97 |- | '''Sub5''' (total reads count)||30||23||234||223||328703||76||61 |- | '''Sub6''' (total reads count)||24||10||68||112||94||59667||31 |- | '''Sub7''' (total reads count)||135||184||69||86||75||21||87004 |- | '''Exp1-3''' (total reads count)||20||16||251||383||1226||301||326 |- | '''Reads mapping rate'''||94.87||93.7||93.15||89.35||84.81||81.47||79.41 |- | '''Mapping to probe rate'''||78.7||82.1||79.6||58.8||18.75||10.05||30.25 |- | '''%of set did not capture'''||0.95%||0.54%||0.63%||0.57%||19.17%||41.12%||39.16% |- | '''Set size'''||3470||3509||30240||30922||30789||13351||7211 |- |}
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