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data_overview:data_overview [2015/07/15 20:01] ceisenhart Major changes under way, please let me finish before doing more |
data_overview:data_overview [2015/07/18 19:24] ceisenhart |
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===== 2015 Data ===== | ===== 2015 Data ===== | ||
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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. | ||
| Data set | Description | Location | | | Data set | Description | Location | | ||
- | |[[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/ | |
- | | [[HiSeq data 2| HiSeq data SW018_S1_L007]] | 2x100bp reads from a single HiSeq lane with 597bp insert size | | + | | [[data_overview::2015::HiSeq data 2| 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 1| HiSeq data SW019_S2_L008]] | 2x100bp reads from a single HiSeq lane with 374bp insert size | | + | | [[data_overview::2015::HiSeq data 1| 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/ | |
- | | [[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-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_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_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/ | |
- | | [[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/ | |
- | |[[ 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/ | |
- | |[[ 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/ | |
- | |[[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/ | |
==== Wet-lab procedures ==== | ==== Wet-lab procedures ==== | ||
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==== Analysis of processed data==== | ==== Analysis of processed data==== | ||
- | [[data_overview::kmergenie | kmergenie Output Showing Kmer Distribution ]] | ||
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- | [[data_overview::preqc | PreqC of adapter-trimmed and PCR duplicate-removed data ]] | ||
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- | [[data_overview::fastQC | FastQC of adapter-trimmed and PCR duplicate-removed data ]] | ||
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- | ===== 2012 Data ===== | + | [[data_overview::2015::analysis::kmergenie | kmergenie Output Showing Kmer Distribution ]] |
- | [[computer_resources:assemblies:mitochondrion| Mitochondrion assembly]] - Generated in 2012 | + | [[data_overview::2015::analysis::preqc | PreqC of adapter-trimmed and PCR duplicate-removed data ]] |
+ | [[data_overview::2015::analysis::fastQC | FastQC of adapter-trimmed and PCR duplicate-removed data ]] | ||
+ | ===== 2011 Data ===== | ||
+ | ===== 2010 Data ===== | ||