Athurva Gore/LabNotes/2009-8-12
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Probe Generation[edit]
- DONE
- KKESH72
- CURRENTLY RUNNING:
- FlyDup901
- FlyDup936
- RPLCACRD
- CpG-SNP set (with 80 bp gap)
- TO RERUN:
- FlyDup5279
- LeeCancer (on opposite strand to target cDNA)
- LeeXGenes (on opposite strand to target cDNA)
- ZhangSNP (on opposite strand to target cDNA)
- TDMR Set (Also check if out-of-memory happens again...maybe run on Miner?)
IPS and Cancer[edit]
- DF6-9-9 IPS line has preliminary data available.
- Lane 1 is IPS, Lanes 2 and 3 are the corresponding fibroblast (Lane 3 has no size-selection)
- Located on genome-miner in:
- /home/kunzhang/Exome/Solexa/090805_HL003
- Dr. Zhang wrote two scripts for preliminary processing
- /home/kunzhang/Exome/scripts/variantCallerSoapSam.pl - calls consensus sequence using SOAP and SAM
- /home/kunzhang/Exome/scripts/pileup2variantsPair.pl - identifies variations present given two consensus sequences
- http://docs.google.com/present/edit?id=0AZnKSQ9Jqu6_ZDVqcWd6cF80NGRiOGZrNWNn&hl=en
- Lane 2 has many more homozygous calls than Lane 3
- EITHER:
- (A) Lane 3 has many more sequencing errors
- OR:
- (B) Lane 2 is only amplifying one allele.
- Dr. Zhang thinks it is option (A). I am not sure how size selection could do this; investigate.