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lecture_notes:04-07-2010

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lecture_notes:04-07-2010 [2010/04/09 00:33]
mpcusack
lecture_notes:04-07-2010 [2010/04/09 19:51]
galt
Line 78: Line 78:
   * For each position, turn image data into a base (AGCT) and a quality score.   * For each position, turn image data into a base (AGCT) and a quality score.
   * Quality means something different on each platform and sometimes even each instrument (Sanger).   * Quality means something different on each platform and sometimes even each instrument (Sanger).
 +    (Correction to what I said in lecture: quality values are **supposed** to be -10 log<​sub>​10</​sub>​ P(error), but calibration is sometimes not very accurate. --- //​[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/04/09 07:18//)
   * May have initial (known) sequences that are used to calibrate quality.   * May have initial (known) sequences that are used to calibrate quality.
  
Line 189: Line 190:
 === Quality === === Quality ===
  
- * Base-space and color-space comes with quality scores. +  ​* Base-space and color-space comes with quality scores. 
- * Flowspace does not have such? have to check. +  * Flowspace does not have such? have to check. 
- * SFS format is the flowspace format for input into the Newbler assembler. ​Does it have any independent ​quality ​measurement?+  * SFS format is the flowspace format for input into the Newbler assembler. ​It has quality ​scores for each base using standard -log10 probability. 
 + 
 +([[http://​www.ncbi.nlm.nih.gov/​Traces/​trace.cgi?cmd=show&​f=formats&​m=doc&​s=format#​sff|SFF format]])
  
 A large number of the assemblers throw away the quality data or only use it later. ​ Some use it to just throw away reads with low quality. A large number of the assemblers throw away the quality data or only use it later. ​ Some use it to just throw away reads with low quality.
lecture_notes/04-07-2010.txt · Last modified: 2015/09/14 18:40 by 68.180.230.228