Athurva Gore/LabNotes/2010-1-27

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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