lecture_notes:04-30-2010
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lecture_notes:04-30-2010 [2010/05/02 06:04] galt created |
lecture_notes:04-30-2010 [2010/05/02 22:01] jstjohn |
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| Should add a mappers section on the tools page. | Should add a mappers section on the tools page. | ||
| - | Next week will be student presentations. | + | Next week will be student presentations. We need volunteers to do presentations. Especially the people who haven't yet presented on an assembler or mapper. |
| Presentations should include the algorithms, | Presentations should include the algorithms, | ||
| Line 146: | Line 146: | ||
| Contiglengths.rdb can give an estimate of coverage. | Contiglengths.rdb can give an estimate of coverage. | ||
| - | back to .join. | + | Back to .join.\\ |
| - | 3 2 is the same as -2 -3 | + | 3 2 is the same as -2 -3\\ |
| - | -7 20 === -20 7 | + | -7 20 === -20 7\\ |
| - | If you flip the pair, the direction an order switch. | + | If you flip the pair, the direction an order switch.\\ |
| - | If he has - - , he just flips it to have + +. | + | If he has - - , he just flips it to have + +.\\ |
| - | chose to put the lower-number contig first. | + | Chose to put the lower-number contig first.\\ |
| The last column is useful but misleading. | The last column is useful but misleading. | ||
| Line 158: | Line 158: | ||
| where would | where would | ||
| - | ----------- | + | "-----------" |
| - | ----------- | + | "-----------" |
| - | + | "-------| |------" | |
| - | -------| |------ | + | "----------" |
| - | ---------- | + | "---------" |
| - | --------- | + | |
| If you pretend they were all at the average length, | If you pretend they were all at the average length, | ||
| Line 181: | Line 180: | ||
| Significance values are tough because of various problems. | Significance values are tough because of various problems. | ||
| - | In one case, | + | In one case, ended up with 40 contigs and only 3 could be properly mapped. |
| - | Ended up with 40 contigs and only 3 could be properly mapped. | + | |
| For inversions, flip and look for reads across boundaries. | For inversions, flip and look for reads across boundaries. | ||
| Line 304: | Line 302: | ||
| ===== Homework for Wednesday ===== | ===== Homework for Wednesday ===== | ||
| - | Do the contig alignments from the .join file. | + | Do the contig alignments from the .join file.\\ |
| (Kevin had already re-done the map-colorspace5.) | (Kevin had already re-done the map-colorspace5.) | ||
lecture_notes/04-30-2010.txt · Last modified: 2010/05/05 21:05 by jmagasin
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