Athurva Gore/LabNotes/2009-8-24
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Probe Sets
- FLYDUP5279 has finished; all old probesets are done
- Need to create and send invoice to Zymo today
- Also mention that probe generation can be rerun without quality filters?
- Need to redo TDMR set and Cpg-SNP set, but with a new probe design...
- Constrain arm+target size to 105 bp
- Then modify P2MIP_v9 to use a 45 bp total arm size
- This will allow library construction to not be necessary
- During capture, MME1 digestion removes 17-18 bp from each side of H1_TARGET_H2
- Should ideally leave us with 75 bp segment remaining, 60 bp of which will be target
- This can be read in the sequencer without library construction, allowing for a much quicker and more efficient experimental procedure
Exome Read Analysis
- Turns out that HL_003 had very poor focus quality. Cannot trust the data because of this, as calls may have been mislocated.
- Flowcell was reused for HL_006; same capturing experiment, but much higher quality data (microscope was in focus)
- Analyzing reads from HL_006
- Comparing Lane 4 and Lane 5
- Lane 4 - NA12878, size-selected
- Lane 5 - NA12878, no size selection
- Mapped using Bowtie, called SNPs using SAM
- Compared to 1KG and dbSNP
- Results BEFORE ANY FILTERING:
- Lane 4 - Size Selection
- vs 1KG, 4,044 hits, 1,533 misses, 218 miscalls (right location but wrong call)
- vs dbSNP, 4,309 SNPs in dbSNP, 1,492 not in dbSNP
- Lane 5 - No Size Selection
- vs 1KG, 3,935 hits, 21,493 misses, 305 miscalls (right location but wrong call)
- vs dbSNP, 4,411 SNPs in dbSNP, 21,328 not in dbSNP
- Lane 4 - Size Selection