Tiling Array Update README for NCBIv36
Affymetrix Tiling Array Support is provided periodically to update the annotations and probe mappings  for tiling arrays with new genome builds.  

Overview
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Tiling Array support has two parts:

1) Updated BPMAP Files to new Genome builds.  (bpmap.zip files)
Provides current genome probe coordinates for analysis software such as Tiling Analysis Software (TAS) Suite. 

In the NCBIv36 release, Updated BPMAP Files are provided for:
        Human and Mouse Whole Genome Tiling Array Sets
        Human and Mouse Promoter Tiling Arrays 

Updated BPMAP files are also provided for C. elegans tiling arrays to Genome release ce4 (Jan 2007).


2) Probe and AnnotaitionBED files (bed.zip files)
Contain array content information in form of genome coordinates of the Tiling Array probes 
for use with genome browsers and table browsers.  

Note: Because of the size of the files, it can take 30 minutes to download them or to load them into a web application.  The individual files are distributed in gzip form (*.gz) which will load onto UCSC more quickly.

In the NCBIv36 release, Probe BED files are provided for:
       Human and Mouse Tiling Arrays
       Human and Mouse Promoter Tiling Arrays
       C elegans Tiling Array
       Arabidopsis Tiling Array
       Drosophila 2.0 Tiling Array
       S. cerevesiae Tiling Array

Also included for Human and Mouse Promoter Arrays:
Annotation BED files are provided which defines NCBIv36 promoter regions and corresponding accessions.  

The Annotation Interval file maps the promoter regions to accession for the Exon, Gene and IVT arrays (HuEx or MoEx, HuGene or MoGene, HG-U133 or MOE430 respectively).  

Details
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1) Updated BPMAP files
Where provided, updated BPMAP files are created with liftOver.*

Rather than remap each probe coordinate to the new genome build, liftOver uses correspondences between two genome sequences to transform the coordinates of the probes from one build to the next.

A whitepaper describing the BPMAP update process is available on the Tiling Array Library File Update Page.

*http://www.soe.ucsc.edu/~kent/exe/linux/liftOver.gz
liftOver is also available as a web application:
http://genome.ucsc.edu/cgi-bin/hgLiftOver

2) Probe BED Files
To visualize Tiling Array content, a Browser Extensible Data (BED) file is provided that reflects the probe coordinates in the new genome builds.

BED files for Tiling Array Sets are provided in both as a single master file and a separate file for each Array in the set.

The Probe BED files are not intended for use by TAS, but allow users to use a variety of 
other available tools. The UCSC genome browser at UCSC (http://genome.ucsc.edu/cgi-bin/hgGateway/) can use the BED files, allowing users to compare their data tracks to a variety of annotations collected there.

BED files are compressed with gzip for easier transfer to the UCSC browser site.

For a full description of the file format, see:
http://genome.ucsc.edu/FAQ/FAQformat#format1  

Notes
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1) Design Region (dr) files used for enrichment analysis in TAS are discontinued.

The Design Region and Annotation BED Files provided for previous updates are now deprecated. 
Tiling users are encouraged to use the annotation collections available at UC Santa Cruz (http://genome.ucsc.edu/) and BioMART (http://www.biomart.org/).
