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lecture_notes:04-07-2010 [2010/04/09 14:21] karplus added correction for mistake I made in class about meaning of quality |
lecture_notes:04-07-2010 [2010/04/11 16:01] karplus changed log10 to -10 log<sub>10</sub> |
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=== 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. |