High Throughput Genome Builds: Difference between revisions

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<LI>agpToDb builds to to RepeatMasking, include data staging ?  SAN, scratch, iscratch</LI>
<LI>agpToDb builds to to RepeatMasking, include data staging ?  SAN, scratch, iscratch</LI>
<LI>masker with or without repeat library</LI>
<LI>masker with or without repeat library</LI>
<LI>makeXxxTrack</LI>
<LI>do BlastzChainNet</LI>
<LI>Conservation</LI>
<LI>make goldenPath downloads</LI>
</UL>
</UL>



Revision as of 22:22, 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, all.joiner, READMEs, liftOvers
  • HTML Pages
  • Links and Clickthroughs