Athurva Gore/LabNotes/2009-8-27
Jump to navigation
Jump to search
[edit]
To Do[edit]
- Forms for Tech Transfer Office
- Invoice for Zymo
Library-free Probesets[edit]
- Investigate TDMR crash today; can we just skip that one site?
IPS and Cancer[edit]
- 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[edit]
- 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[edit]
- 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[edit]
- 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