Athurva Gore/LabNotes/2009-8-27: Difference between revisions

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>Ajgore
(New page: {{ AGLabEntry|2009-8-26|2009-8-28 }} =To Do= * Forms for Tech Transfer Office * Invoice for Zymo =Library-free Probesets= * Investigate TDMR crash today; can we just skip that one site? ...)
 
>Ajgore
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** Reducing quality scores of end bases when SNPs found
** Reducing quality scores of end bases when SNPs found
** Reducing quality scores of all end bases
** Reducing quality scores of all end bases
* Looked at HL006_s5 data
** Wanted to compare the small number of misses remaining to 1000 genome.
* Found that if a coverage filter of >4 is set,
hits misses miscalls
Total Number
29      111        7
Number with coverage < 4:
4      86        7
* Lose only four hits, but eliminate most of the misses and all of the miscalls!
* This makes sense, as with coverage < 4 (2 or 3 reads), we cannot be certain of the site.

Revision as of 18:12, 27 August 2009

Navigation

To Do

  • Forms for Tech Transfer Office
  • Invoice for Zymo

Library-free Probesets

  • Investigate TDMR crash today; can we just skip that one site?

IPS and Cancer

  • Want to test various trimming methods to see which works best.
    • Removing end bases from reads with SNPs
    • Removing end bases from all reads
    • Reducing quality scores of end bases when SNPs found
    • Reducing quality scores of all end bases
  • Looked at HL006_s5 data
    • Wanted to compare the small number of misses remaining to 1000 genome.
  • Found that if a coverage filter of >4 is set,
hits misses miscalls
Total Number		
29      111        7
Number with coverage < 4:		
4       86         7
  • Lose only four hits, but eliminate most of the misses and all of the miscalls!
  • This makes sense, as with coverage < 4 (2 or 3 reads), we cannot be certain of the site.