High Throughput Genome Builds: Difference between revisions

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<UL>
<UL>
<LI>Downloads</LI>
<LI>Downloads</LI>
<LI>Metadata, hgCentral, dbDb, all.joiner, READMEs</LI>
<LI>Metadata, hgCentral, defaultDb, dbDb, all.joiner, READMEs</LI>
<LI>liftOvers (between same species)</LI>
<LI>liftOvers (between same species)</LI>
<LI>HTML Pages</LI>
<LI>HTML Pages</LI>
<LI>Links and Clickthroughs</LI>
<LI>Links and Clickthroughs</LI>
</UL>
</UL>

Revision as of 22:24, 30 May 2006

Input Requirements

AGP File, Sequence

Output Tracks

Gap. Gold, ChromInfo, GC5

Then Repeat Masking/Window Masker and trfBig

Produces rmsk/windowMask and simpleRepeats track

Early Tracks

Genscan, Genbank Scripts, CpG Islands

Map Closest protein set (human mostly)

Same Species LiftOvers

Comparative Genomics

human and mouse

Candidate Genomes

(A)platypus(new + update), (A)frog update, (A)Stickleback(fish)(new + update), (A)Medaka(fish), (B)rhesus update, (B)chicken update, (A)elephant, (B)rabbit(new + update), (A)pig(new + update), (B)cat(new + update), (A)fugu update, (B)chimp update, (C)mouse, (C)human

Tools

  • xxxToAgp
  • agpToDb builds to to RepeatMasking, include data staging ? SAN, scratch, iscratch
  • masker with or without repeat library
  • makeXxxTrack
  • do BlastzChainNet
  • Conservation
  • make goldenPath downloads

Bugs

.html pages for tracks

QA Time

  • Downloads
  • Metadata, hgCentral, defaultDb, dbDb, all.joiner, READMEs
  • liftOvers (between same species)
  • HTML Pages
  • Links and Clickthroughs