High Throughput Genome Builds: Difference between revisions
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<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>makeXxxTrack</LI> | <LI>masker with or without repeat library | ||
<LI>doBlastzChainNet (how about saving run-time parameters in a metadata DB table to create README/.html information ?)</LI> | <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</LI> | <LI>Conservation</LI> | ||
</UL> | </UL> | ||
Revision as of 22:48, 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
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
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
| Organism | Assembly | matrix | gaps | abridged repeats | ...etc... |
|---|---|---|---|---|---|
| mouse | mm8 | medium | medium | yes | ...etc... |
| human | hg19 | loose | loose | no | ...etc... |
