Athurva Gore/LabNotes/2010-1-7: Difference between revisions

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Line 11: Line 11:
** HL027
** HL027
** HL030
** HL030
** AL006
* Need to find the mapping rate for each one; can guess its usefulness in the data set this way.
* Need to find the mapping rate for each one; can guess its usefulness in the data set this way.
** Should we incorporate older reads?
** Should we incorporate older reads?
Line 22: Line 23:
| align="center" style="background:#f0f0f0;"|'''Mapped Downsampled Reads'''
| align="center" style="background:#f0f0f0;"|'''Mapped Downsampled Reads'''
|-
|-
| HL013||||||||
| HL013||1||59491092||||
|-
|-
| HL014||||||||
| HL014||6||47862784||||
|-
|-
| HL015||||||||
| HL015||1||53717748||||
|-
|-
| HL019||||||||
| HL019||4||59623024||||
|-
|-
| HL024||||||||
| HL024||1||64242556||||
|-
|-
| HL025||||||||
| HL025||1||36424692||||
|-
|-
| HL027||||||||
| HL027||8||47824792||||
|-
|-
| HL028||||||||
| HL028||6||37242492||||
|-
|-
| HL029||||||||
| HL029||1||33484628||||
|-
|-
| HL030||||||||
| HL030||1||58820868||||
|-
| AL006||5||57942248||||
|-
|-
|
|}
|}



Latest revision as of 19:24, 8 January 2010

PGP[edit]

  • If we only use data from October or newer, we have the following data sets:
    • HL013
    • HL024
    • HL025
    • HL029
    • HL019
    • HL014
    • HL028
    • HL015
    • HL027
    • HL030
    • AL006
  • Need to find the mapping rate for each one; can guess its usefulness in the data set this way.
    • Should we incorporate older reads?
  • Map one lane from each flowcell to get a general idea of mapping rate.
    • Fill in the below table:
Flowcell Lane Number of Reads Mapped Reads Mapped Downsampled Reads
HL013 1 59491092
HL014 6 47862784
HL015 1 53717748
HL019 4 59623024
HL024 1 64242556
HL025 1 36424692
HL027 8 47824792
HL028 6 37242492
HL029 1 33484628
HL030 1 58820868
AL006 5 57942248

iPS and Cancer[edit]

  • Waiting to hear back from Science
    • First advisor didn't really seem to read paper
    • If no response, try with Nature
  • Rewriting as Letter to Nature
    • Guidelines: LINK
    • ~200 word introductory paragraph, ~1500 word text, ~300 word methods summary, ~1000 word methods, and supplementary info
  • Mostly done with rewrite; need to go over text of paper and edit the additions made