User Manual focusing on main TiMAT processing pipeline; written with version 3.4
Please note: due to file format changes with TiMAT's *cela and *celp files, versions 3.2 and later are not backwards compatible with earlier versions.TiMAT package v3.4.4 (15 January 08) - TiMAT_3.4.4.zip
|tpmap file, dmel release 4.0, for 7G||7GUnique.tpmap.bz2|
|tpmap file, dmel release 4.0, for pre 7G||pre7GUnique.tpmap.bz2|
|1lQ file, needed for remapping and chip QC||dmelTilingArray.1lq.bz2|
|Affymetrix's unmodified bpmap file, dmel release 3.1, pre 7G||antiSense.bpmap.bz2|
|A BLAST filtered bpmap file, dmel release 4.0, pre 7G||antiSenseBlastFilteredRel4.0.bpmap.bz2|
|A BLAST scored bpmap file, dmel release 4.0, pre 7G||antiSenseBlastScoredRel4.0.bpmap.bz2|
|Combine GFF3 gene annotation, dmel release 4.0||dmel4.0Annotation.gff3.bz2|
|A gold standard list of CG genes with verified cDNAs||goldStandardCGGeneList.txt.bz2|
|Fasta chromosome files, dmel release 4.3||dmel-all-chromosome-r4.3.fasta.bz2|
|Affymetrix's binary bpmap to text bpmap-like conversion tool (Windows)||ProbeExporterV2.zip|
|Affymetrix's binary cel to text cel conversion tool (Windows)||CelFileConversion.zip|
(To force a download, try right-clicking or holding down the option key while clicking a link.)
TiMAT ©2005, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Technology Transfer Department at TTD@lbl.gov referring to "TiMAT (LBNL Ref CR-2109)"
NOTICE. This software was developed under funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.