SNP Track QA: Difference between revisions

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(starting wiki page about QAing SNPs)
 
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If you have any general questions about snps this is a good resource: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpsnpfaq
This page is no longer maintained.
 
*  updateTimes.csh
: make sure have most recent version
 
*  makedoc
: located at src/hg/makeDb/doc/{build}.txt
: make sure that exists in makedoc
 
* look at mysql tables
: check that the number of exceptions listed in snp###Exceptions and snp###ExceptionDesc match
: make sure that there are no exceptions in the snp###Exceptions that do not also exist in the snp###ExceptionDesc table
: If possible, compare to old SNP tracks for this species. Look for radical jumps in rows or particular types of SNPs.
: check that func types in snp### table are documented in the html, both in the methods and in the check boxes. If there are new func types, make sure they are displayed correctly in the browser
: check that the weights column in snp### are only 1,2 or 3
: look the names of the snps. Make sure that they make sense (no extraneous ones, all lower case, etc).
 
*  check settings (hgTrackUi and clicking on individual snp)
: make sure that all settings that you can select for are present in mysql tables and vice versa
: make sure that methods mention all func types that you can select in trackUi
: check that can turn different gene tracks on in the trackUi
 
*  all details for one data point (click through everything)
 
*  featureBits, featureBits gap, countPerChrom.csh, and checkCoverage.csh
: Look at featureBits/Coverage for main snp table as well as the dbCoding and the ortho table. Also check coverage of haplo chromosomes.
: see how coverage compares to old snp track if possible. Also when open up the track, most snps should match to the same place (though some will change)
 
*  index
: click "show sizes" in PushQ
 
*  runJoiner.csh
 
*  checkOffend.csh
: check to see if any items off end of chromosome for all tables
 
*  performance
: make sure appropriate entries in hgFindSpec (this is very important for snps since the table is so large). Check that entries in hgFindSpec work by searching for some snps.
: make sure track "turns off" when viewing large regions (table too large to load for large regions)
: look at large snp insertions/deletions and check that display correctly in hgTracks and hgTrackUi
: check that display looks good
: positionalTblCheck - script that checks to see if the table is ordered for faster access
 
*  description
: check spelling and grammar
: make sure external files mentioned at the end of the html page exist at ncbi
: emails sanitized
 
*  default position - is it turned on by default?
 
*  table descriptions - view table schema
 
*  release log and release log url
 
 
==AT RELEASE BE SURE TO:==
# push tableDescriptions and hgFindSpec
# edit trackDb.ra so that old snp track is hidden by default if needed
# make announcement on genome announce
# notify Mark D so he can update LS-SNP
# notify Galt so he can default to most current snp track in genome graphs

Latest revision as of 19:32, 10 March 2011

This page is no longer maintained.