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data_overview:data_overview [2015/07/15 20:16]
ceisenhart Major changes under way, please let me finish before doing more
data_overview:data_overview [2015/07/28 06:29]
ceisenhart ↷ Page moved from data_overview to data_overview:data_overview
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 The raw data locations are listed below. However many of these files have been processed through Skewer/​fastUniq and a variety of other programs. To see and download these '​processed'​ files please view the data set page.  The raw data locations are listed below. However many of these files have been processed through Skewer/​fastUniq and a variety of other programs. To see and download these '​processed'​ files please view the data set page. 
 | Data set | Description | Location |  | Data set | Description | Location | 
-| [[data_overview::​MiSeq data| MiSeq data SW019_S1_L001]] | 2x300bp reads from a single MiSeq lane | +| [[data_overview::2015::MiSeq data| MiSeq data SW019_S1_L001]] | 2x300bp reads from a single MiSeq lane | http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Data/​2015/​MiSeq-data-SW019_S1_L001 ​
-| [[data_overview::​HiSeq data 2| HiSeq data SW018_S1_L007]] | 2x100bp reads from a single HiSeq lane with 597bp insert size | +| [[data_overview:​2015:hiseq_sw018_s1| HiSeq data SW018_S1_L007]] | 2x100bp reads from a single HiSeq lane with 597bp insert size | http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Data/​2015/​HiSeq-data-SW018_S1_L007 ​
-| [[data_overview::​HiSeq data 1| HiSeq data SW019_S2_L008]] | 2x100bp reads from a single HiSeq lane with 374bp insert size | +| [[data_overview:​2015:hiseq_sw019_s2| HiSeq data SW019_S2_L008]] | 2x100bp reads from a single HiSeq lane with 374bp insert size |http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Data/​2015/​HiSeq-data-SW019_S2_L008 ​
-| [[data_overview::​UCSF_BS-MK | UCSF BS-MK data]] | 2x250bp reads with 450-650bp insert size | +| [[data_overview::2015::​UCSF_BS-MK | UCSF BS-MK data]] | 2x250bp reads with 450-650bp insert size |http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Data/​2015/​UCSF_BS-MK ​
-| [[data_overview::​UCSF_BS-tag | UCSF BS-tag data]] | 2x250bp reads with 375-575bp insert size | +| [[data_overview::2015::​UCSF_BS-tag | UCSF BS-tag data]] | 2x250bp reads with 375-575bp insert size |http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Data/​2015/​UCSF_BS-tag ​
-| [[data_overview::​UCSF_SW018 | UCSF SW018 Data]] | 2x250bp reads from SW018 library | +| [[data_overview::2015::​UCSF_SW018 | UCSF SW018 Data]] | 2x250bp reads from SW018 library ​|http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Data/​2015/​UCSF_SW018 ​
-| [[data_overview::​UCSF_SW019 | UCSF SW019 Data]] | 2x250bp reads from SW019 library | +| [[data_overview::2015::​UCSF_SW019 | UCSF SW019 Data]] | 2x250bp reads from SW019 library ​|http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Data/​2015/​UCSF_SW019 ​
-| [[data_overview::​Lucigen mate-pair data]] | 2x300bp reads, expected insert size is greater than 1kb | +| [[data_overview::2015::Lucigen mate-pair data]] | 2x300bp reads, expected insert size is greater than 1kb |http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Data/​2015/​Lucigen-mate-pair ​
-| [[data_overview::​SW041 | SW041 mate-pair data ]] | 2x76bp reads, expected insert size is 3-4kb | +| [[data_overview::2015::SW041 | SW041 mate-pair data ]] | 2x76bp reads, expected insert size is 3-4kb |http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Data/​2015/​SW041-mate-pair ​
-| [[data_overview::​SW042 | SW042 mate-pair data ]] | 2x76bp reads, expected insert size is 5-6kb | +| [[data_overview::2015::SW042 | SW042 mate-pair data ]] | 2x76bp reads, expected insert size is 5-6kb |http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Data/​2015/​SW042-mate-pair ​
-| [[data_overview::​RNA-Seq | RNA-Seq data]] | Preliminary data generated as of 06/12/15 | +| [[data_overview::2015::RNA-Seq | RNA-Seq data]] | Preliminary data generated as of 06/​12/​15 ​| http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Data/​2015/​RNA_Seq ​|
  
 ==== Wet-lab procedures ==== ==== Wet-lab procedures ====
  
 The shotgun library preparation protocol used was provided by Steven Weber, ​ The shotgun library preparation protocol used was provided by Steven Weber, ​
-[[Steven Weber'​s Notes on Lab Prep]]+[[data_overview:​steven_weber_s_notes_on_lab_prep]]
  
 {{:​meyer_kircher.pdf|Library Prep Protocol }} {{:​meyer_kircher.pdf|Library Prep Protocol }}
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 ==== Analysis of processed data==== ​ ==== Analysis of processed data==== ​
-[[data_overview::​kmergenie | kmergenie Output Showing Kmer Distribution ]] 
  
-[[data_overview::​preqc PreqC of adapter-trimmed and PCR duplicate-removed data ]]+[[data_overview::​2015::​analysis::​kmergenie ​kmergenie Output Showing Kmer Distribution ​]]
  
-[[data_overview::​fastQC ​FastQC ​of adapter-trimmed and PCR duplicate-removed data ]] +[[data_overview::​2015::​analysis::​preqc ​PreqC of adapter-trimmed and PCR duplicate-removed data ]]
- +
- +
-===== 2012 Data ===== +
- +
-[[computer_resources:​assemblies:​mitochondrion| Mitochondrion assembly]] - Generated in 2012+
  
 +[[data_overview::​2015::​analysis::​fastQC | FastQC of adapter-trimmed and PCR duplicate-removed data ]]
 +===== 2011 Data =====
  
 +===== 2010 Data =====
  
  
  
  
data_overview/data_overview.txt · Last modified: 2015/07/28 06:29 by ceisenhart