Athurva Gore/LabNotes/2010-1-27: Difference between revisions
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** Uses PGP4, PGP6, and PGP10 old data (from before last September; probably only reliable good data from that time period) | ** 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 | ** Uses HL034 PGP5 data with sliding trimmer 10 | ||
{| {{table}} | {| {{table border=1}} | ||
| align="center" style="background:#f0f0f0;"|'''Sample''' | | align="center" style="background:#f0f0f0;"|'''Sample''' | ||
| align="center" style="background:#f0f0f0;"|'''Reads''' | | align="center" style="background:#f0f0f0;"|'''Reads''' | ||
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| align="center" style="background:#f0f0f0;"|'''dbSNP %''' | | align="center" style="background:#f0f0f0;"|'''dbSNP %''' | ||
|- | |- | ||
| PGP1||73,656,659||52,445,891||0.71||22,543,941||'''78%'''|| | | 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%|| | | 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%|| | | 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%'''|| | | 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%'''|| | | 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%'''|| | | PGP6||86,066,955||58,086,066||0.67||21,177,467||'''73%'''||94.14% | ||
|- | |- | ||
| PGP7||28,619,340||15,398,503||0.54||12,730,873||44%|| | | PGP7||28,619,340||15,398,503||0.54||12,730,873||44%||94.16% | ||
|- | |- | ||
| PGP8||116,237,040||61,363,238||0.53||20,930,980||'''72%'''|| | | PGP8||116,237,040||61,363,238||0.53||20,930,980||'''72%'''||94.60% | ||
|- | |- | ||
| PGP9||117,277,366||55,399,638||0.47||20,805,413||'''72%'''|| | | PGP9||117,277,366||55,399,638||0.47||20,805,413||'''72%'''||94.47% | ||
|- | |- | ||
| PGP10||55,310,684||35,456,916||0.64||19,759,504||'''68%'''|| | | PGP10||55,310,684||35,456,916||0.64||19,759,504||'''68%'''||88.97% | ||
|} | |} |
Revision as of 00:22, 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) | 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
- We can use these new data sets to obtain new coverage statistics as well.
- Uses data from previous table (add link), all sliding trimmer 5
- 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 | 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 | 12,730,873 | 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 | 20,805,413 | 72% | 94.47% |
PGP10 | 55,310,684 | 35,456,916 | 0.64 | 19,759,504 | 68% | 88.97% |