Method
Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays
1 Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
2 Swiss Institute of Bioinformatics, Genopode Building, CH-1015 Lausanne, Switzerland
3 Lausanne DNA Array Facility, Center for Integrative Genomics, University of Lausanne, Genopode Building, CH-1015 Lausanne, Switzerland
4 Section of Integrative Biology and Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station C0930, Austin, Texas 78712, USA
Genome Biology 2010, 11:R4 doi:10.1186/gb-2010-11-1-r4
Published: 12 January 2010Additional files
Additional file 1:
Distribution of the read coverage for the five Arabidopsis chromosomes across the different accessions.
Format: PDF Size: 365KB Download file
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Additional file 2:
Experimentally tested deletions predicted in Eil-0 and Tsu-1, positions and primer sequences.
Format: XLS Size: 32KB Download file
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Additional file 3:
Number of unique tiles from the Col-0 genome without UHTS coverage in the four accessions for different tiling array signal ratios.
Format: PDF Size: 89KB Download file
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Additional file 4:
Deletions predicted from paired end reads of the Eil-0 and Lc-0 genomes by the Breakdancer algorithm.
Format: XLS Size: 377KB Download file
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Additional file 5:
Genes carrying deletions as predicted from intersection of UHTS and tiling arrays.
Format: XLS Size: 149KB Download file
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Additional file 6:
The subset of genes whose coding sequence is carrying deletions as predicted from intersection of UHTS and tiling arrays.
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Additional file 7:
Script for computing the UHTS coverage and signal ratio of array tiles.
Format: R Size: 4KB Download file
Additional file 8:
Script for deletion prediction based on intersection of UHTS coverage and tiling array signal.
Format: R Size: 3KB Download file
