ENCODE QA Checklist

Other functions of use? wigTableStats.sh bigWigSummary bigWigInfo

Getting Started

1. Check kent/src/hg/makeDb/doc/encodeDccHg18/*.txt to determine if/how the file diverges from reality.
2. Make a list of all tables (new & updated that need to be pushed to beta)
3. Run qaEncodeTracks.csh and check output
4. Do bigPush.csh using list created above
5. Remove "release alpha" lines from subtracks in trackDb.wgEncode.ra
6. Push any new .wib or .bb files from hgwdev to hgnfs1 if applicable

Description Page

1. Read description page
2. Make sure there is a link to the help doc (in the config section)
3. Check that there is metadata by clicking on the "..." link in the tables list
4. Is description page detailed enough?
5. Is description page are the citations in correct format?
6. Does the "Display Conventions and Configuration" section cover all track types?
7. Test all hyper-links on description page.
8. Test configuration section
9. Test multi-view matrix
10. Test "reset to defaults" button
11. Make sure there's a link to the ENCODE Data Release Policy

Other things to check

1. Run genePredCheck/pslCheck if applicable. (i.e. if your track is a gene prediction track)
2. Release log: Check to be sure the release log entry is right.
3. Make sure the tracks in the Tier1 and Tier2 Cell Lines are properly colored (no black, and all tracks from one Cell Line have the same color).
4. Make sure your track is listed on the downloads page - (push from hgwdev -> hgwbeta, RR) /usr/local/apache/htdocs/ENCODE/downloads.html

Files

hgdownloads

1. make sure there is a preamble.html file in the /releaseN directory
2. index.html
   1. For releaseN: run the encodeDownloadsPage.pl script directly in the /releaseN directory to generate a new index.html page
   2. Make sure this file is executable (because of the way the links are created)
   3. Preamble should include brief description and link to the trackUi
   4. should include a link to the files.txt and md5sum.txt files
   5. For releaseN: should also include the release number at end of description
   6. should contain the name of each file being released

Pushing Files

1. Push gbdb Files: hgwdev -> hgnfs1 (i.e. /gbdb/hg18/wib/wgEncode*.wib)
2. Push other Files: hgwdev -> hgwbeta & RR (i.e. /usr/local/apache/htdocs/ENCODE/protocols/cell/*.pdf)
3. Push download Files: hgwdev -> hgdownload (i.e. /usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncode*/*) (Note: no releaseN directory on hgdownload)
4. After Pushing Files: check push with: checkPushedFiles.csh

Testing in the Browser

1. Test one point from table to view in GB
2. Zoom into base level (at different visibilities)
3. Zoom way out 1million bps (at different visibilities)
4. Searching: should items be searchable?
5. default visibility: should this track be on by default?
6. Check URL in Release Log (should go to track description page)
7. Check for lab contact (sanitize email addresses using encodeEmail.pl script)
8. Does the first 'Signal' subtrack pass the chr1 test (chr1 loads in less than one minute)
9. Do all views for one experiment pass chr1 test (e.g. Pol2 in GM12878 cells)?
10. Test the performance in a gene-size region of the track with just the default-on subtracks

Releasing to RR

1. Check the trackDb diffs to see if there is any reason that <db>.trackDb can't go out today
2. If you determine that it's OK to push <db>.trackDb, then write to browser-qa "hands off <db>.trackDb"
3. Check release log field in PushQ...needs to start with ENCODE
4. Push track tables from mysqlbeta -> mysqlrr (not trackDb yet)
5. Drop tables from hgwbeta that need to be removed (being replaced by V2 tables)
6. Clean up trackDb (remove blocks for the dropped tables - currently marked release beta)
7. Make strict for <db> on hgwbeta and check to make sure tracks look like you expect them to (all there and accounted for)
8. Drop tables being removed from the RR
9. Push trackDb, tableDescriptions and, if items are searchable (not usually for Encode), hgFindSpec
10. Push download files and index.html (from hgwdev to hgdownload)
11. Drop download files that need to be dropped (from hgdownload)
12. Drop .wib files that need to be dropped (from hgnfs1)
13. If necessary edit and push ENCODE/downloads.html from hgwdev -> hgwbeta & RR
14. Push cv.ra file (only if there is a matrix)
15. Cc the data wrangler for this track on all your pushes Cc encode@soe.ucsc.edu on your final push