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 [2015/09/14 18:40] 68.180.230.228 ↷ Links adapted because of a move operation |
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| * 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]]. | ||
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| Do not run anything on the headnode for campusRocks. | Do not run anything on the headnode for campusRocks. | ||
| Learn how to use sungrid to tell it how to run it on (one of) the nodes. Alternatively, use the [[http://campusrocks.soe.ucsc.edu/ganglia/|status page]] to find an idle node and ssh to it directly. | Learn how to use sungrid to tell it how to run it on (one of) the nodes. Alternatively, use the [[http://campusrocks.soe.ucsc.edu/ganglia/|status page]] to find an idle node and ssh to it directly. | ||
| - | The [[computer_resources:campusrocks|campusrocks page]] has a link to some documentation on sungrid. | + | The [[archive:computer_resources:campusrocks|campusrocks page]] has a link to some documentation on sungrid. |
| We should all have access now to campusrocks. If you don't contact tech staff (IT request). | We should all have access now to campusrocks. If you don't contact tech staff (IT request). | ||
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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, 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 18:40 by 68.180.230.228
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