Minimal browser

From Genecats
Revision as of 19:30, 11 October 2012 by Rhead (talk | contribs) (changed genbank tracks required per discussion w/ braney and jim (also http://redmine.soe.ucsc.edu/issues/7668))
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For browser for a new organism (not an update to an existing browser), at least these tracks must exist:

  • sequence
  • repeat masker
  • gold/gap assembly tracks
  • genbank mRNAs & ESTs (if available; see /data/genbank/data/organism.lst for counts)
  • Other RefSeq (xenoRefGene)
  • BLAT/PCR servers
  • CPG Islands
  • Genscan

And here's a list of tracks for a "pretty good" browser (these are strongly recommended if it's going to be part of a multiple alignment):

  • all of the "minimal" tracks listed above
  • Transmap (mapping gene set from closest well-annotated organism)
  • ENSEMBL Genes (if available)
  • Human Proteins
  • Human chain/net (at least human, if not others)
  • 3-8-way multiple alignment
  • Self Chain track for "finished" assemblies (e.g. human, mouse, zebrafish)
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