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>< | <TR><TD>mouse</TD><TD>mm8</TD><TD>medium</TD><TD>medium</TD><TD>yes</TD><TD>...etc...</TD></TR> | ||
<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
| Organism | Assembly | matrix | gaps | abridged repeats | ...etc... |
|---|---|---|---|---|---|
| mouse | mm8 | medium | medium | yes | ...etc... |
| human | hg19 | loose | loose | no | ...etc... |
