Athurva Gore/LabNotes/2010-1-27: Difference between revisions
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* 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. | ||
* The dbSNP percentage is still very close to the one found in the other libraries. | * The dbSNP percentage is still very close to the one found in the other libraries. | ||
** We can use | * 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: |
Revision as of 23:58, 27 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% |
- 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: