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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 |
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* 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. | ||
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=== 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. |
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+ | ([[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. |