User Tools

Site Tools


lecture_notes:04-07-2010

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Last revision Both sides next revision
lecture_notes:04-07-2010 [2010/04/08 17:33]
mpcusack
lecture_notes:04-07-2010 [2010/04/11 15:47]
learithe
Line 14: Line 14:
   * Discusses Overlap and de-Bruijn graphs.   * Discusses Overlap and de-Bruijn graphs.
  
-454 Newbler assembler is entirely proprietary and almost nothing is known on how it works internally.+454 Newbler assembler is entirely proprietary and almost nothing is known on how it works internally ​(The only description is in the supplementary material of the original 454 method paper ((Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005.|http://​dx.doi.org/​10.1038/​nature03959)).
  
 Christy Hightower wants more feedback on the tools, to say good/​bad. ​ Feedback should be added to the wiki [[lecture_notes:​04-02-2010|lecture notes for her lecture]]. Christy Hightower wants more feedback on the tools, to say good/​bad. ​ Feedback should be added to the wiki [[lecture_notes:​04-02-2010|lecture notes for her lecture]].
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, flow-space, ​and color-space ​all come with quality scores. 
- * 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?+SFF format is the flowspace format for input into the Newbler assembler. ​It has quality ​scores for each base using standard -10 log<​sub>​10</​sub>​ 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 11:40 by 68.180.230.228