Athurva Gore/LabNotes/2010-1-27
Jump to navigation
Jump to search
PGP Data[edit]
HL034 PGP5 Data[edit]
- 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) | 11,260,366 | 19,924,839 | 19,866,529 |
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[edit]
- We can use these new data sets to obtain new coverage statistics as well.
- Uses data from previous table for PGP1-6, PGP8, PGP10 (add link), sliding trimmer 5
- Uses data from previous table for PGP7 and PGP9 (add link), sliding trimmer 10
- Uses PGP4, PGP6, and PGP10 old data (from before last September; probably only reliable good data from that time period)
- Uses HL034 PGP5 data with sliding trimmer 10
Sample | Reads | Usable Reads | Percent Usable | CCDS Coverage (cov 8, qual 30) | Percent CCDS Covered | dbSNP % |
PGP1 | 73,656,659 | 52,445,891 | 0.71 | 22,543,941 | 78% | 95.22% |
PGP2 | 13,777,534 | 8,201,178 | 0.6 | 9,964,899 | 35% | 95.26% |
PGP3 | 19,642,850 | 12,512,635 | 0.64 | 11,716,319 | 40% | 94.54% |
PGP4 | 101,486,098 | 57,569,270 | 0.57 | 21,358,854 | 74% | 94.42% |
PGP5 | 50,460,039 | 28,632,469 | 0.65 | 19,866,529 | 69% | 94.34% |
PGP6 | 86,066,955 | 58,086,066 | 0.67 | 21,177,467 | 73% | 94.14% |
PGP7 | 28,619,340 | 15,398,503 | 0.54 | 12,535,785 | 44% | 94.16% |
PGP8 | 116,237,040 | 61,363,238 | 0.53 | 20,930,980 | 72% | 94.60% |
PGP9 | 117,277,366 | 55,399,638 | 0.47 | 20,677,998 | 72% | 94.47% |
PGP10 | 55,310,684 | 35,456,916 | 0.64 | 19,759,504 | 68% | 88.97% |
PGP2, PGP3, PGP7[edit]
- Have new data from HL035 for these sets
- Currently mapping two lanes of PGP2 and two lanes of PGP3
- Still need to map the one lane of PGP7; make sure to use slidingTrimmer 10
- Can then merge in, see how many bases we have