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.