High Throughput Genome Builds: Difference between revisions

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This is a transcript of whiteboard notes from the 5/30/06 Genecats meeting.
==Input Requirements==
==Input Requirements==


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(B)rhesus update, (B)chicken update, (A)elephant, (B)rabbit(new + update), (A)pig(new + update),
(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
(B)cat(new + update), (A)fugu update, (B)chimp update, (C)mouse, (C)human
Key:
(A) = Abbreviated browser only
(B) = More expanded browser
(C) = Full browser


==Tools==
==Tools==
<UL>
<UL>
<LI>xxxToAgp</LI>
<LI>xxxToAgp</LI>
<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>masker with or without repeat library</LI>
<P>verifies AGP & Sequence, sets up unmasked sequence into 500K chunks for RM, stores sequence in standard place.</P></LI>
<LI>masker with or without repeat library
<P>Work towards windowMask automation</P></LI>
<LI>Masked sequence stager</LI>
<LI>make goldenPath downloads</LI>
<LI>makeXxxTrack
<P>Work towards track by track automation</P></LI>
<LI>doBlastzChainNet (how about saving run-time parameters in a metadata DB table to create README/.html information ?)
<P>chain/net .html file $alignSettings keyword and library function to make alignment parameter table</P></LI>
<LI>Conservation (On all browsers ?)</LI>
</UL>
</UL>


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<UL>
<UL>
<LI>Downloads</LI>
<LI>Downloads</LI>
<LI>Metadata, hgCentral, all.joiner, READMEs, liftOvers</LI>
<LI>Metadata, hgCentral, defaultDb, dbDb, all.joiner, READMEs</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>
==Metadata blastz parameter 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><TD>mouse</TD><TD>mm8</TD><TD>medium</TD><TD>medium</TD><TD>yes</TD><TD>...etc...</TD></TR>
<TR><TD>human</TD><TD>hg19</TD><TD>loose</TD><TD>loose</TD><TD>no</TD><TD>...etc...</TD></TR>
</TABLE>
[[Category:Technical FAQ]]
[[Category:Automation]]

Latest revision as of 23:18, 21 August 2006

This is a transcript of whiteboard notes from the 5/30/06 Genecats meeting.

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

Key: (A) = Abbreviated browser only (B) = More expanded browser (C) = Full browser

Tools

  • xxxToAgp
  • agpToDb builds to to RepeatMasking, include data staging ? SAN, scratch, iscratch

    verifies AGP & Sequence, sets up unmasked sequence into 500K chunks for RM, stores sequence in standard place.

  • masker with or without repeat library

    Work towards windowMask automation

  • Masked sequence stager
  • make goldenPath downloads
  • makeXxxTrack

    Work towards track by track automation

  • doBlastzChainNet (how about saving run-time parameters in a metadata DB table to create README/.html information ?)

    chain/net .html file $alignSettings keyword and library function to make alignment parameter table

  • Conservation (On all browsers ?)

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...
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