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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==Map Closest protein set (human mostly)== | ==Map Closest protein set (human mostly)== | ||
==Same Species LiftOvers== | |||
==Comparative Genomics== | ==Comparative Genomics== | ||
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==Candidate Genomes== | ==Candidate Genomes== | ||
platypus(new + update), frog update, Stickleback(fish)(new + update), Medaka(fish), | (A)platypus(new + update), (A)frog update, (A)Stickleback(fish)(new + update), (A)Medaka(fish), | ||
rhesus update, chicken update, elephant, rabbit(new + update), pig(new + update), | (B)rhesus update, (B)chicken update, (A)elephant, (B)rabbit(new + update), (A)pig(new + update), | ||
cat(new + update), fugu update, chimp 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== | |||
<UL> | |||
<LI>xxxToAgp</LI> | |||
<LI>agpToDb builds to to RepeatMasking, include data staging ? SAN, scratch, iscratch | |||
<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> | |||
==Bugs== | |||
.html pages for tracks | |||
==QA Time== | |||
<UL> | |||
<LI>Downloads</LI> | |||
<LI>Metadata, hgCentral, defaultDb, dbDb, all.joiner, READMEs</LI> | |||
<LI>liftOvers (between same species)</LI> | |||
<LI>HTML Pages</LI> | |||
<LI>Links and Clickthroughs</LI> | |||
</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
| Organism | Assembly | matrix | gaps | abridged repeats | ...etc... |
|---|---|---|---|---|---|
| mouse | mm8 | medium | medium | yes | ...etc... |
| human | hg19 | loose | loose | no | ...etc... |
