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{{ AGLabEntry|2009-8-26|2009-8-28 }} =To Do= * Forms for Tech Transfer Office * Invoice for Zymo =Library-free Probesets= * Investigate TDMR crash today; can we just skip that one site? =IPS and Cancer= * Want to test various trimming methods to see which works best. ** Removing end bases from reads with SNPs ** Removing end bases from all reads ** Reducing quality scores of end bases when SNPs found ** Reducing quality scores of all end bases ==NA12878== * Looked at HL006_s5 data ** Wanted to compare the small number of misses remaining to 1000 genome. * Found that if a coverage filter of >4 is set, hits misses miscalls Total Number 29 111 7 Number with coverage < 4: 4 86 7 * Lose only four hits, but eliminate most of the misses and all of the miscalls! ** This makes sense, as with coverage < 4 (2 or 3 reads), we cannot be certain of the site. ==DF-6-9-9== * Hoping to get a filter that allows good coverage but has ~5% of SNPs outside dbSNP only * Can we accomplish this simply by thresholding coverage? * Looked at DF699 from HL004 with a 5-bp tossout range. ** Has more hits; want to see if we can filter misses at this stage. ** If we filter by coverage < 4: ** Lose 2108/11314 hits, 666/2139 misses * We do better if we cut out more reads (with a 15-bp tossout range) ** Lose 1944/11314 hits (9370), 1040/2139 misses (1099) * Investigating the reads is probably a better strategy, though post-processing out low-coverage SNPs is probably not a bad idea. =Trimming bad reads= * Wrote a script that behaves in the same way as the rejectBadLigation.pl, but instead trims reads down to the correct size * Takes a variable input as well * With DF699 from HL004, reduces error. ** 10061 hits, 1376 misses ** Not as much reduction as removing reads; more hits kept, however
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