SNP Track QA: Difference between revisions

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Starting with snp132, the SNP track was split into 4 tracks, [http://genome.ucsc.edu/goldenPath/newsarch.html#041811.2 announced here]. If you have any general questions about snps this is a good resource: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpsnpfaq.  In addition to the SNP-specific checks on this page, be sure to follow the [[New_track_checklist | new track checklist]], too.
Starting with snp132, the SNP track was split into 4 tracks, [http://genome.ucsc.edu/goldenPath/newsarch.html#041811.2 announced here]. If you have any general questions about snps this is a good resource: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpsnpfaq.  In addition to the SNP-specific checks on this page, be sure to follow the [[New_track_checklist | new track checklist]], too.


* look at mysql tables
==mysql tables==
** 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.
* 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 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
* check that the weights column in snp### are only 1,2 or 3
** look at the exceptionDesc table: spot-check the counts, make sure the exception messages show up on hgc pages, make sure the descriptions make sense.  Ideally, this table would be visible in the Table Browser when the track is selected, but it isn't right now.  See [http://redmine.soe.ucsc.edu/issues/3606 Redmine #3606] for current status of this problem.
* look at the exceptionDesc table: spot-check the counts, make sure the exception messages show up on hgc pages, make sure the descriptions make sense.  Ideally, this table would be visible in the Table Browser when the track is selected, but it isn't right now.  See [http://redmine.soe.ucsc.edu/issues/3606 Redmine #3606] for current status of this problem.




* check settings
==settings==
** make sure that all settings that you can select for are present in mysql tables and vice versa
* make sure that all settings that you can select for are present in mysql tables and vice versa
** try some table browser queries that use the checkboxes on the filter page
* try some table browser queries that use the checkboxes on the filter page
** try turning on selected gene tracks on track controls page, make sure results show up
* try turning on selected gene tracks on track controls page, make sure results show up
   in "UCSC's predicted function relative to selected gene tracks:"
   in "UCSC's predicted function relative to selected gene tracks:"
** try the various color options
* try the various color options


* check details
==check details==
** be sure to include a snp with chimera and ls-snp links in your testing.  To find such a SNP, look in the lsSnpPdb, and then check the links under "Mappings to PDB protein structures" on the track details page.
* be sure to include a snp with chimera and ls-snp links in your testing.  To find such a SNP, look in the lsSnpPdb, and then check the links under "Mappings to PDB protein structures" on the track details page.
** make sure the tracks "turn off" when viewing large regions (these tables are too large to load for large regions)
* make sure the tracks "turn off" when viewing large regions (these tables are too large to load for large regions)




*  description
==description==
** note that most of the description is the same on all 4 snp tracks -- this is kept in one file (snp132.shared.html for snp132) that is included in the other html with a line like <pre><!--#insert file="sharedText.html"--></pre>
* note that most of the description is the same on all 4 snp tracks -- this is kept in one file (snp132.shared.html for snp132) that is included in the other html with a line like <pre><!--#insert file="sharedText.html"--></pre>
** make sure the source files listed are correct and exist at ncbi
* make sure the source files listed are correct and exist at ncbi
** make sure that methods section mentions all func types that you can select in trackUi
* make sure that methods section mentions all func types that you can select in trackUi


* downloads - If this is a human assembly, make sure there are downloads for "Masked FASTA Files (human assemblies only)"  Check hat the FASTA files are actually masked with snps.  Look for some lines with y, w, m, etc. Can use a command like:
==downloads==
If this is a human assembly, make sure there are downloads for "Masked FASTA Files (human assemblies only)"  Check hat the FASTA files are actually masked with snps.  Look for some lines with y, w, m, etc. Can use a command like:
   zcat chr1.subst.fa.gz | head -300 | grep -i [^atgcn]
   zcat chr1.subst.fa.gz | head -300 | grep -i [^atgcn]


* check with Galt to make sure that the current snp track will be used in genome graphs.  (rsID is one of the accepted [http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html#Format genome graphs formats].  When rsIDs are entered, their positions are looked up in the snp table.  Galt said in April 2011 that currently: "It starts looking for snp134, then snp133, ... down to about snp125. The first one it finds that exists in the db is returned and used for resolving user symbols that might be rsIds."
==genome graphs==
Check with Galt to make sure that the current snp track will be used in genome graphs.  (rsID is one of the accepted [http://genome.ucsc.edu/goldenPath/help/hgGenomeHelp.html#Format genome graphs formats].  When rsIDs are entered, their positions are looked up in the snp table.  Galt said in April 2011 that currently: "It starts looking for snp134, then snp133, ... down to about snp125. The first one it finds that exists in the db is returned and used for resolving user symbols that might be rsIds."




Revision as of 00:55, 23 April 2011

Starting with snp132, the SNP track was split into 4 tracks, announced here. If you have any general questions about snps this is a good resource: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helpsnpfaq. In addition to the SNP-specific checks on this page, be sure to follow the new track checklist, too.

mysql tables

  • 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 at the exceptionDesc table: spot-check the counts, make sure the exception messages show up on hgc pages, make sure the descriptions make sense. Ideally, this table would be visible in the Table Browser when the track is selected, but it isn't right now. See Redmine #3606 for current status of this problem.


settings

  • make sure that all settings that you can select for are present in mysql tables and vice versa
  • try some table browser queries that use the checkboxes on the filter page
  • try turning on selected gene tracks on track controls page, make sure results show up
 in "UCSC's predicted function relative to selected gene tracks:"
  • try the various color options

check details

  • be sure to include a snp with chimera and ls-snp links in your testing. To find such a SNP, look in the lsSnpPdb, and then check the links under "Mappings to PDB protein structures" on the track details page.
  • make sure the tracks "turn off" when viewing large regions (these tables are too large to load for large regions)


description

  • note that most of the description is the same on all 4 snp tracks -- this is kept in one file (snp132.shared.html for snp132) that is included in the other html with a line like 
    <!--#insert file="sharedText.html"-->
  • make sure the source files listed are correct and exist at ncbi
  • make sure that methods section mentions all func types that you can select in trackUi

downloads

If this is a human assembly, make sure there are downloads for "Masked FASTA Files (human assemblies only)" Check hat the FASTA files are actually masked with snps. Look for some lines with y, w, m, etc. Can use a command like: 

  zcat chr1.subst.fa.gz | head -300 | grep -i [^atgcn]

genome graphs

Check with Galt to make sure that the current snp track will be used in genome graphs. (rsID is one of the accepted genome graphs formats. When rsIDs are entered, their positions are looked up in the snp table. Galt said in April 2011 that currently: "It starts looking for snp134, then snp133, ... down to about snp125. The first one it finds that exists in the db is returned and used for resolving user symbols that might be rsIds."


AT RELEASE BE SURE TO:

  • make the old SNP track (if any) hidden by default, and check to see if any old SNP tracks should be dropped from the RR.
  • announce the release on genome-announce.
  • when you push the snp-masked downloads, add a link to downloads.html.
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