Athurva Gore/LabNotes/2010-1-27: Difference between revisions
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{| {{table border=1}} | {| {{table border=1}} | ||
| align="center" style="background:#f0f0f0;"| | | align="center" style="background:#f0f0f0;"| | ||
| align="center" style="background:#f0f0f0;"|'''HL013 | | align="center" style="background:#f0f0f0;"|'''HL013, HL025, SlideTrim5''' | ||
| align="center" style="background:#f0f0f0;"|'''HL013 | | align="center" style="background:#f0f0f0;"|'''HL013, HL025, ''HL034'', SlideTrim5''' | ||
| align="center" style="background:#f0f0f0;"|'''HL013 | | align="center" style="background:#f0f0f0;"|'''HL013, HL025, ''HL034'', SlideTrim10''' | ||
|- | |- | ||
| dbSNP||align="right"|4071||align="right"|8643||align="right"|8093 | | dbSNP||align="right"|4071||align="right"|8643||align="right"|8093 | ||
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| dbSNP%||align="right"|95.16%||align="right"|93.13%||align="right"|94.34% | | dbSNP%||align="right"|95.16%||align="right"|93.13%||align="right"|94.34% | ||
|- | |||
| CCDS Coverage (cov8, qual30)||align="right"|11260366||align="right"|19924839||align="right"|19866529 | |||
|- | |||
| Percent CCDS (cov8, qual 30)||align="right"|39%||align="right"|68.7%||align="right"|68.5% | |||
|} | |} | ||
* Using the sliding trimmer with a 10 bp cutoff seems to fix the issue. | * Using the sliding trimmer with a 10 bp cutoff seems to fix the issue. |
Revision as of 00:03, 28 January 2010
PGP Data
HL034 PGP5 Data
- Got some new PGP5 data from HL034
- Dr. Zhang tried to map it; ended up with a very low dbSNP percentage (~70%)
- Can we fix it with some trimming?
- Tried sliding trimmer 5 and 10
- Merged it into the previous data
- Got the following results:
HL013, HL025, SlideTrim5 | HL013, HL025, HL034, SlideTrim5 | HL013, HL025, HL034, SlideTrim10 | |
dbSNP | 4071 | 8643 | 8093 |
notdbSNP | 207 | 638 | 486 |
dbSNP% | 95.16% | 93.13% | 94.34% |
CCDS Coverage (cov8, qual30) | 11260366 | 19924839 | 19866529 |
Percent CCDS (cov8, qual 30) | 39% | 68.7% | 68.5% |
- Using the sliding trimmer with a 10 bp cutoff seems to fix the issue.
- The dbSNP percentage is still very close to the one found in the other libraries.
- Not sure what happened
- Same library works earlier with sliding trimmer 5, but now requires sliding trimmer 10?
- Something to do with flowcell?
New PGP Coverage Summary
- We can use these new data sets to obtain new coverage statistics as well: