Athurva Gore/LabNotes/2009-8-25
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ProbeSet Generation
- Currently creating TDMR set and CpGSNP set with new no-library-construction protocol
- This requires a constraint of arms+target = 105
- This will allow reads of 60-80 bp (after digestion) to cover the entire fragment, greatly improving the capturing protocol (as it seems that library construction is a major source of headaches)
NA12878 False Positives
- Noticed that many misses have high number of start/end sites for reads
- Checked actual read mapping; it seemed that the end of reads was causing the most trouble
- Many reads had several SNPs in the last few bases
- After discussing with Dr. Zhang, decided to test mapping and SNP calling using the following protocol.
- Reads were inspected after mapping to see if any SNPs were present in bases 36-40
- If any SNPs were present, the entire read was thrown out
- Hypothesis: Junk is getting ligated onto the ends of reads during library construction
- If we remove the junk reads, we should be able to greatly improve the false positive rate
- Remapped and SNP-called the HL006 s_4 (size-selected) and s_5 (not size-selected) sets
- Filtered out clonal reads
- Removed reads that had SNPs in locations >= the 36th base
- Wanted to see if false positive rate went down (though since entire reads are being rejected, coverage will decrease and therefore false negative rate will go up)
- Results: