The University of Arizona
TCW Documentation Index
AGCoL | TCW Home | Doc Index | singleTCW Guide | DE Guide | multiTCW Guide | Tour
Getting started
  Summary A summary of the input, processing and suite of programs.
  InstallationInstalling TCW and other necessary and optional software.
  
Major documents with step-by-step details using the Demo dataset
  Single species runSingleTCW - Building a single species annotated TCW database
  Differential Expression runDE - Add DE to the singleTCW database
  Multiple species runMultiTCW - Building a comparison database from single TCW databases
  
Annotation details
  Annotation Setup UniProt and GO for use with TCW, plus using other databases for annotation
  Search annoDB Using the super-fast diamond or ublast in place of blast
  ORF finder Description of options, algorithm, outputs, and results.
  Updating annotation Removing, adding, updating annotation
  
Other docs
  External SoftwarePackages used by TCW
  TCW Tour Snapshots of different TCW screens
  Assembly Details Not typically necessary1
  Mac-OSX Installing MySQL, etc on Mac-OSX
  Trouble Shooting Potential technical difficulties.
  Release NotesRelease detail since v1.0
  HelpAll TCW programs have Help pop-ups on every display.
1TCW cannot be used for high-throughput sequenceing reads (e.g. Illumina). It is typically used with transcripts, proteins or mRNA (e.g. predicted genes with introns removed), i.e. no assembly necessary. However, it is still occassionally useful for Sanger ESTs or assembling multiple sets of transcripts.

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