SNP Track QA: Difference between revisions

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m (adding Category:Browser QA tracks)
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# notify Galt so he can default to most current snp track in genome graphs
# notify Galt so he can default to most current snp track in genome graphs


[[Category:Browser_QA]][[Category:Browser QA tracks]]
[[Category:Browser QA tracks]]

Revision as of 03:11, 23 July 2010

If you have any general questions about snps this is a good resource: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpsnpfaq

  • 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 tables for this species. Look for big jumps in the number of different func types of SNPs as well as the number and type of exceptions.
    • 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). The checkHgFindSpec tool with the -checkTermRegex option will check that all of the names in the snp### table match the regular expression specified in trackDb. There is not an option to run it on a single table, so just run it on the whole database and look for output specific to the snp table. For instance:
 checkHgFindSpec -checkTermRegex hg19
  • 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 (or runBits.chs which does both featureBits and 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
  • checkTableCoords
    • look for illegal genome coordinates for all positional 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:

  1. push tableDescriptions and hgFindSpec
  2. edit trackDb.ra so that old snp track is hidden by default if needed
  3. make announcement on genome announce
  4. notify Mark D so he can update LS-SNP
  5. notify Galt so he can default to most current snp track in genome graphs