Array Analysis - Array Design Files

Tools for your cytogenomic microarray practice, including ICCG (formerly ISCA) design files and custom tracks to aid in analysis.

BED files - ISCA v2 Array .bed files

These files contain the oligo coverage for the different ISCA array designs. Available in NCBI36/hg18 and in GRCh37/hg19. Last updated June 2012.

BED files - ISCA v2 Targeted Regions .bed files

These files contain the targeted regions for the different ISCA array designs. Available in both NCBI36/hg18 and GRCh37/hg19. Last updated June 2012.

XML files - ISCA Clinical Design .xml files (NCBI36/hg18)

These files are the ISCA Clinical array design files to be used in Agilent software programs.

(NOTE: These files are large. To download, please right-click on the link and select "Save Target As". For the Agilent ISCA v2 designs, we have altered the design files to aid in data interpretation for clinical use. These files are called ISCA v2 Clinical designs. For the 180K Clinical design, oligos in regions of large segmental duplications have been eliminated from the design file and will not be visualized using Agilents software. For all arrays, oligos that had two perfect mappings in the PARs are only displayed on chrX, not on chrY. In DNA Analytics/Genomic Workbench, do not select the Expand Non-unique probes option in the Tools section. These files are in hg18 genome build.)

XML files - ISCA 44K v1 Design file

This is the .xml design file for the ISCA 44K version 1 design