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archive:summer_2015 [2015/06/09 12:51] karplus [Agenda Items] added details to some tasks |
archive:summer_2015 [2015/06/10 00:14] jolespin |
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|Christopher Kan|chkan@ucsc.edu|SGA|Pogson|Will finish SGA Assembly| | |Christopher Kan|chkan@ucsc.edu|SGA|Pogson|Will finish SGA Assembly| | ||
| Nedda | nsaremi@ucsc.edu | SOAP | Green | | | Nedda | nsaremi@ucsc.edu | SOAP | Green | | ||
+ | | Josh | jolespin@ucsc.edu | SGA | Bernick |Once a good assembly is generated and we get a transcriptome, I can extract the exons, introns, and genes (5'UTR, CDS, 3'UTR). I wrote some scripts that can do this and confirms with exon-junction motifs| | ||
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* Use of old data (2010 and 2011 classes: There is not really much data there, and the quality is not very high, so there may not be much point in trying to use it. Perhaps mapping it could find some variation—we might like to know whether the UCSC slug population is nearly clonal. | * Use of old data (2010 and 2011 classes: There is not really much data there, and the quality is not very high, so there may not be much point in trying to use it. Perhaps mapping it could find some variation—we might like to know whether the UCSC slug population is nearly clonal. | ||
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+ | Longer term: we'll need to decide whether we need more data, particularly for scaffolding. Will Ed's lab be continuing to develop a new mate-pair library procedure, which could give us new libraries to work with? Will the MinION deliver higher-throughput long reads this year, and can we get a run of long DNA through the MinION? | ||
====Finished Work==== | ====Finished Work==== |