Athurva Gore/LabNotes/2009-8-18: Difference between revisions
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>Ajgore (New page: {{ AGLabEntry|2009-8-17|2009-8-19 }} =Probe Generation= * '''DONE''' ** KKESH72 ** RPLCACRD ** CpG-SNP set (with 80 bp gap) ** FlyDup936 ** A-to-I Probes for Erez and Billy ** LeeCancer (...) |
>Ajgore |
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* Currently: | * Currently: | ||
** Running script to separate our SNP calls and 1KG SNP calls by in-range and out-of-range | ** Running script to separate our SNP calls and 1KG SNP calls by in-range and out-of-range | ||
* For our SNP calls: | |||
** FOUND THAT 3190/20762 were NONSPECIFIC | |||
** ~85% specific capture | |||
* Want to separate false positives from true positives in our SNPs. | * Want to separate false positives from true positives in our SNPs. | ||
* NEXT STEP: | * NEXT STEP: |
Revision as of 16:59, 18 August 2009
Probe Generation
- DONE
- KKESH72
- RPLCACRD
- CpG-SNP set (with 80 bp gap)
- FlyDup936
- A-to-I Probes for Erez and Billy
- LeeCancer (on opposite strand to target cDNA)
- LeeXGenes (on opposite strand to target cDNA)
- ZhangSNP (on opposite strand to target cDNA)
- CURRENTLY RUNNING:
- FlyDup901
- FlyDup5279
- TO RERUN:
- TDMR Set (Also check if out-of-memory happens again...maybe run on Miner?)
- Look into this tomorrow
- TDMR Set (Also check if out-of-memory happens again...maybe run on Miner?)
Exome SNPs - NA12878
- Currently:
- Running script to separate our SNP calls and 1KG SNP calls by in-range and out-of-range
- For our SNP calls:
- FOUND THAT 3190/20762 were NONSPECIFIC
- ~85% specific capture
- Want to separate false positives from true positives in our SNPs.
- NEXT STEP:
- Look at IPS data; plot quality and coverage of SNPs.
- Run bowtie on runs from NA12878 that have high false positives
- See if there is a pattern; can we separate these false positives out somehow?