Athurva Gore/LabNotes/2010-1-8: Difference between revisions
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=PGP= | =PGP= | ||
==Estimated Mapping Rate== | |||
* Dataset mapping table (October through now): | * Dataset mapping table (October through now): | ||
** HL013 to HL030 | ** HL013 to HL030 | ||
Line 32: | Line 33: | ||
| HL030||1||58820868||14705217||8827261||8492613||0.6||0.58 | | 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== | |||
* We can use this to predict how many usable reads we have for each data set. | * We can use this to predict how many usable reads we have for each data set. | ||
** Count of reads for each PGP sample: | ** Count of reads for each PGP sample: | ||
{| {{table border=1}} | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Reads''' | |||
| align="center" style="background:#f0f0f0;"|'''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== | |||
* 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= | |||
=IPS and Cancer= | |||
* 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. |
Latest revision as of 00:58, 9 January 2010
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.