Athurva Gore/LabNotes/2009-8-27

From ZhangLabWiki
Revision as of 18:13, 27 August 2009 by >Ajgore (→‎IPS and Cancer)
Jump to navigation Jump to search

Navigation

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?