Athurva Gore/LabNotes/2010-1-27
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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: