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
