Athurva Gore/LabNotes/2010-1-8

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PGP[edit]

Estimated Mapping Rate[edit]

  • Dataset mapping table (October through now):
    • HL013 to HL030
Flowcell Lane Reads Times 4 Number of Reads Mapped Reads Mapped Downsampled Reads Mapping Rate % Usable Reads
HL013 1 59491092 14872773 12555897 8987088 0.84 0.6
HL014 6 47862784 11965696 8324230 5959697 0.7 0.5
HL015 1 53717748 13429437 9839373 6031436 0.73 0.45
HL019 4 59623024 14905756 8695192 8691338 0.58 0.58
HL024 1 64242556 16060639 14817937 13563313 0.92 0.84
HL025 1 36424692 9106173 8077318 6247035 0.89 0.69
HL027 8 47824792 11956198 9269899 8819601 0.78 0.74
HL028 6 37242492 9310623 5979563 4630087 0.64 0.5
HL029 1 33484628 8371157 3396996 3355959 0.41 0.4
HL030 1 58820868 14705217 8827261 8492613 0.6 0.58
AL006 5 57942248 14485562 10565704 9604607 0.73 0.66

Estimated Number of Reads Usable[edit]

  • We can use this to predict how many usable reads we have for each data set.
    • Count of reads for each PGP sample:
Sample Reads Estimated Usable Reads
PGP1 73,656,659 58,630,458
PGP2 13,777,534 8,325,274
PGP3 19,642,850 12,613,974
PGP4 39,022,194 21,228,150
PGP5 18,620,501 12,083,551
PGP6 44,542,386 23,913,315
PGP7 28,619,340 17,384,463
PGP8 116,237,040 63,690,701
PGP9 117,277,366 60,695,633
PGP10 26,108,372 13,478,483
  • How much coverage will this get us?
    • Map a few data sets and check?

Test Coverage[edit]

  • PGP1 is done; can merge once mapping/downsampling/slidingTrim for other sets is done
  • Will then start:
    • PGP2 (only a few datasets; "lower end") - DONE
    • PGP4 (middle of the road) - DONE
  • Can hopefully get an idea of "# of reads -> how much coverage at read depth 8 and quality 30"
  • Mapping is done, now merge all lanes for the 3 PGP flowcells into one file for each
    • Then check what our coverage looks like and what our dbSNP percentage is for each case
  • Currently merging data

PGP Paper[edit]

IPS and Cancer[edit]

  • Finish up Nature Letter draft.
    • Need to fix methods section so it sounds better.
    • Need to cut down online methods by ~700 words
    • Need to go over main text, make sure it still sounds ok
  • Then, send to Dr. Zhang by end of this weekend.