lecture_notes:04-30-2010
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lecture_notes:04-30-2010 [2010/05/02 06:09] galt |
lecture_notes:04-30-2010 [2010/05/02 22:05] 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 23: | Line 23: | ||
| 2 students per day would be fine. | 2 students per day would be fine. | ||
| If it takes longer, that's fine. | If it takes longer, that's fine. | ||
| + | |||
| + | Volunteers for Monday: | ||
| + | Installing, Running, How does it work in general? | ||
| + | Find out which have gotten done and which have not. | ||
| + | Mark off which have been done on the list. (apr 5) | ||
| + | |||
| + | Shorty maybe should be on the list. | ||
| + | The idea of using the matepaired or paired end data | ||
| + | to make a group in a cluster and then to assemble that. | ||
| + | Let's add Shorty to the list of tools. | ||
| + | |||
| + | Maybe we don't have anyone ready for Monday, | ||
| + | you need to be ready to do it in the next two weeks. | ||
| + | You can tell me or send me email. | ||
| ==== Literature ==== | ==== Literature ==== | ||
| Line 52: | Line 66: | ||
| papers on assemblers. | papers on assemblers. | ||
| - | ==== Back to Presentations ==== | ||
| - | |||
| - | Volunteers for Monday: | ||
| - | Installing, Running, How does it work in general? | ||
| - | Find out which have gotten done and which have not. | ||
| - | Mark off which have been done on the list. (apr 5) | ||
| - | |||
| - | Shorty maybe should be on the list. | ||
| - | The idea of using the matepaired or paired end data | ||
| - | to make a group in a cluster and then to assemble that. | ||
| - | Let's add Shorty to the list of tools. | ||
| - | |||
| - | Maybe we don't have anyone ready for Monday, | ||
| - | you need to be ready to do it in the next two weeks. | ||
| - | You can tell me or send me email. | ||
| ==== Genome Browser ==== | ==== Genome Browser ==== | ||
| Line 74: | Line 73: | ||
| someone in browser group do a presentation on it. | someone in browser group do a presentation on it. | ||
| - | ==== Homework ==== | + | |
| + | ==== Homework for Wednesday ==== | ||
| Homework assignments, as people have not been contributing | Homework assignments, as people have not been contributing | ||
| equally to the wiki. Those of you who took David Bernick's class | equally to the wiki. Those of you who took David Bernick's class | ||
| will have already done it. Different version of newbler produced | will have already done it. Different version of newbler produced | ||
| different assembly. Order and orient the contigs. Try to do it. | different assembly. Order and orient the contigs. Try to do it. | ||
| + | |||
| + | Do the contig alignments from the .join file.\\ | ||
| + | (Kevin had already re-done the map-colorspace5.) | ||
| ===== map-colorspace5 ====== | ===== map-colorspace5 ====== | ||
| Line 146: | Line 149: | ||
| 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 161: | ||
| 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 180: | Line 183: | ||
| 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 301: | Line 303: | ||
| Even just getting the right answer within a factor of 10 was | Even just getting the right answer within a factor of 10 was | ||
| encouraging. | encouraging. | ||
| - | |||
| - | ===== Homework for Wednesday ===== | ||
| - | Do the contig alignments from the .join file.\\ | ||
| - | (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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