Dinh 2011/NOTES/2011-12-21
Jump to navigation
Jump to search
Re-subsetting DMR220k (w/o Exp1-3)[edit]
- 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
Dataset | Indx1 (Sub1 capture) | Indx2 (Sub2 capture) | Indx3 (Sub3 capture) | Indx4 (Sub4 capture) | Indx5 (Sub5 capture) | Indx6 (Sub6 capture) | 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 |