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{{ 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 (on opposite strand to target cDNA) ** LeeXGenes (on opposite strand to target cDNA) ** ZhangSNP (on opposite strand to target cDNA) ** FlyDup901 * '''CURRENTLY RUNNING:''' ** FlyDup5279 * '''TO RERUN:''' ** TDMR Set (Also check if out-of-memory happens again...maybe run on Miner?) *** Look into this tomorrow * 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. * HL002 has a TON of SNPs. ** 185k! ** Something is very odd here. * Noticed that HL002 and one set from HL003 both used size-selection. ** Not sure about Billy's results * Looked for a homozygous overrepresentation. ** In HL002, definite presence of homozygous SNPs over heterozygous SNPs. * Next Steps: ** Check both of these samples against dbSNP ** Check both of these samples against 1KG ** Is there anything similar among the false positives?
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