Table of Contents

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
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
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
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
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
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
UCSF SW018 Data 2x250bp reads from SW018 library http://genome-test.cse.ucsc.edu/~charles/BME235_backup/Data/2015/UCSF_SW018
UCSF SW019 Data 2x250bp reads from SW019 library http://genome-test.cse.ucsc.edu/~charles/BME235_backup/Data/2015/UCSF_SW019
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
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
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
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, steven_weber_s_notes_on_lab_prep

Library Prep Protocol

Analysis of processed data

kmergenie Output Showing Kmer Distribution

PreqC of adapter-trimmed and PCR duplicate-removed data

FastQC of adapter-trimmed and PCR duplicate-removed data

2011 Data

2010 Data