data_overview:data_overview
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data_overview:data_overview [2015/07/16 18:45] ceisenhart Major changes under way, please let me finish before doing more |
data_overview:data_overview [2015/07/28 06:29] (current) 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::analysis::kmergenie | kmergenie Output Showing Kmer Distribution ]] | + | [[data_overview::2015::analysis::kmergenie | kmergenie Output Showing Kmer Distribution ]] |
| - | [[data_overview::analysis::preqc | PreqC of adapter-trimmed and PCR duplicate-removed data ]] | + | [[data_overview::2015::analysis::preqc | PreqC of adapter-trimmed and PCR duplicate-removed data ]] |
| - | [[data_overview::analysis::fastQC | FastQC of adapter-trimmed and PCR duplicate-removed data ]] | + | [[data_overview::2015::analysis::fastQC | FastQC of adapter-trimmed and PCR duplicate-removed data ]] |
| ===== 2011 Data ===== | ===== 2011 Data ===== | ||
data_overview/data_overview.1437072323.txt.gz · Last modified: 2015/07/16 18:45 by ceisenhart
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