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archive:summer_2015 [2015/06/09 08:25]
karplus [Agenda Items] added longer term questions
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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-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 ​log reads this year, and can we get a run of long DNA through the MinION?+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