High Throughput Genome Builds

From genomewiki
Revision as of 22:05, 30 May 2006 by Hiram (talk | contribs)
Jump to navigationJump to search

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