====== Data ====== 

===== 2015 Data =====

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_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: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: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::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::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::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::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::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::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::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::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 ====

The shotgun library preparation protocol used was provided by Steven Weber, 
[[data_overview:steven_weber_s_notes_on_lab_prep]]

{{:meyer_kircher.pdf|Library Prep Protocol }}


==== Analysis of processed data==== 

[[data_overview::2015::analysis::kmergenie | kmergenie Output Showing Kmer Distribution ]]

[[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 =====