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archive:summer_2015 [2015/06/09 05:51]
karplus [Agenda Items] added details to some tasks
archive:summer_2015 [2015/06/30 07:30]
jaredc [Schedule of meetings]
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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 try and 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. ​ Can't meet weekly since I'll be in SD. |
 +|Robert|calef@soe.ucsc.edu|Discovar|Green|Will start looking into running SOAP gap closer on the Kolossus Discovar assembly, as well as tools for scaffolding with RNA-seq data|
 +|Charles| chkcole@ucsc.edu| Meraculous| Vollmers| I'm currently working on getting the RNA-Seq data. We have some preliminary stuff I just need to process it and confirm the quality of the libraries. Also, repetitive elements.|
  
  
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   * Meet in PSB 305 (same classroom)   * Meet in PSB 305 (same classroom)
   * once a week   * once a week
-  * Weds at 10:30am or 1:30pm+  * Weds at 1:30pm
  
  
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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.
  
 +
 +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====
  
-A list of work completed ​sense BME235 ended.+A list of work completed ​since BME235 ended:
  
   * Disovar assembly with all shotgun data, accomplished on Kolussus   * Disovar assembly with all shotgun data, accomplished on Kolussus
   * SOAPdenovo assembly with all shotgun data and gap closed, accomplished on edser2   * SOAPdenovo assembly with all shotgun data and gap closed, accomplished on edser2
archive/summer_2015.txt · Last modified: 2015/07/18 13:32 by ceisenhart