New Full Genome DATA 10/21/03!!!
See Methods paper for the latest scripts
eXtreme Array Mapping for QTL
This page contains data, scripts, tables and addition figures for
Large Scale Identification of Single Feature Polymorphisms in Complex Genomes
Justin O. Borevitz, David Liang, David Plouffe, Hur-Song Chang, Tong Zhu, Detlef Weigel,
Charles C. Berry, Elizabeth Winzeler, Joanne Chory
Current DNA labeling protocol here
A link to a graphical genome browser showing all the features and which ones are markers
Search At4g10780 as an example and zoom in.
Perl scripts for finding unique features in the genome and mini-micro satellites are in sfp.scripts.zip (fixed 5/8/2004)
A table of all 92924 features and which are markers in Ler, Ws-2, Nd-1, Tsu-1, and Cvi
Large .pdf files of deletions across the genome. Ler, Ws-2, Nd-1, Tsu-1, and Cvi
Let’s get started with the analysis in R (download R)
A link to lcluster R library for calling deletions
A link to bqtl R library that assists ChipMap
Download the setup files.
Follow the readme.txt file in sfp.scripts.zip
You can get the 3 Col and 3 Ler .cel files for AtGenome1 here
You can read the data in, identify SFPs, set permutation threshold,
and confirm SFPs with sequence data, etc. Then do the clustering to identify deletions
Here are the .cel files for accessions (Ws-2,Nd-1,Tsu,and Cvi) and for mapping.
Finally do some mapping.
Enjoy Justin Borevitz & Charles Berry