Athurva Gore/LabNotes/2009-8-18
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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?)
- Check numbering of new probes
- Appears to be slightly inaccurate as well.
- For residue coordinate system:
- End position should be increased by 1
- Start position should be increased by 2
- For space coordinate system:
- End position should be increased by 1
- Start position should be increased by 1
Exome SNPs - NA12878
- Currently:
- Running script to separate our SNP calls and 1KG SNP calls by in-range and out-of-range
- NOTE: File Dr. Zhang provided uses a slightly inaccurate start position; needs to be incremented by 1 for the residue based coordinate system. End is accurate.
Specific vs. Nonspecific capture
- For our SNP calls:
- FOUND THAT 3190/20762 were NONSPECIFIC
- ~85% specific capture
- Want to separate false positives from true positives in our SNPs.
Comparison of our SNP calls to 1KG
- Compared our SNP calls to 1KG
- Found (out of 20,761 SNPs):
- 16319 hits (~78.5%)
- 598 miscalls (~3%)
- 3844 misses (~18.5%)
- Need to determine reasons for this
- Plot of quality and coverage:
NEXT STEPS:
- Look at IPS data; plot quality and coverage of SNPs.
- Run bowtie on runs from NA12878 that have high false positives - Done
- See if there is a pattern; can we separate these false positives out somehow?
NA12878 High False Positive Reads
- Locations
- 07282009_HL002, Lanes 4-7
- 08052009_HL003, Lanes 4-5
- Storing data on genome-miner:/media/TmpStore1/AG_Scratch/Exome/NA12878
- Using this sample for validation
- First step, need to map these reads.
- Start out with reads on a per experiment basis
- Merge s_4 through s_7 in HL002, merge s_4 and s_5 in HL003
- Run Bowtie-SAM script on these merged sets; check results
- Bowtie-SAM has been run on both HL003 and HL002.
- Next Steps:
- Check both of these samples against dbSNP
- Check both of these samples against 1KG
- Is there anything similar among the false positives?