Dinh 2011/NOTES/2011-12-21: Difference between revisions

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>Dinh
(Created page with '==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 ju…')
 
>Dinh
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**Indx1-7 were captured with the individual subsets, however, the amount of probes to target were all the same.
**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 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  
*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
  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
|-
|}

Latest revision as of 04:49, 22 December 2011

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