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
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.