High Throughput Genome Builds: Difference between revisions

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==Metadata blastz parameter table==
==Metadata blastz parameter table==
<TABLE>
<TABLE BORDER=1>
<TR><TH>Organism</TH><TH>Assembly</TH><TH>matrix</TH><TH>gaps</TH><TH>abridged repeats</TH><TH>...etc...</TH></TR>
<TR><TH>Organism</TH><TH>Assembly</TH><TH>matrix</TH><TH>gaps</TH><TH>abridged repeats</TH><TH>...etc...</TH></TR>
<TR><TH>mouse</TH><TH>mm8</TH><TH>medium</TH><TH>medium</TH><TH>yes</TH><TH>...etc...</TH></TR>
<TR><TD>mouse</TD><TD>mm8</TD><TD>medium</TD><TD>medium</TD><TD>yes</TD><TD>...etc...</TD></TR>
<TR><TH>human</TH><TH>hg19</TH><TH>loose</TH><TH>loose</TH><TH>no</TH><TH>...etc...</TH></TR>
<TR><TD>human</TD><TD>hg19</TD><TD>loose</TD><TD>loose</TD><TD>no</TD><TD>...etc...</TD></TR>
</TABLE>
</TABLE>

Revision as of 22:41, 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
  • doBlastzChainNet (how about saving run-time parameters in a metadata DB table to create README/.html information ?)
  • 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


Metadata blastz parameter table

OrganismAssemblymatrixgapsabridged repeats...etc...
mousemm8mediummediumyes...etc...
humanhg19looselooseno...etc...