Conservation Track QA

QAing Conservation and Most Conserved tracks for a new assembly (using the ponAbe2 (orangutan) assembly as an example throughout)

Make a list of tables: multiz8way multiz8wayFrames multiz8waySummary phastCons8way phastConsElements8way seq extFile

Make a list of files to go to hgnfs1: /gbdb/ponAbe2/multiz8way/phastCons8way.wib /gbdb/ponAbe2/multiz8way/anno/maf/*

Make a list of files to go to hgdownload: /usr/local/apache/htdocs/goldenPath/ponAbe2/phastCons8way/*.* /usr/local/apache/htdocs/goldenPath/ponAbe2/phastCons8way/phastConsScores/* /usr/local/apache/htdocs/goldenPath/ponAbe2/multiz8way/*.* /usr/local/apache/htdocs/goldenPath/ponAbe2/multiz8way/maf/*

Make a list of all organisms in the Conservation track: _ orangutan Pan troglodytes July 2007, ponAbe2 _ human Homo sapiens Mar 2006, hg18 _ chimpanzee Pan troglodytes Mar 2006, panTro2 _ rhesus Macaca mulatta Jan 2006, rheMac2 _ marmoset Callithrix jacchus June 2007, calJac1 _ mouse Mus musculus July 2007, mm9 _ opossum Monodelphis domestica Jan 2006, monDom4 _ platypus Ornithorhychus anatinus Mar 2007, ornAna1

Make a list of all organisms for which there are nets & chains: (put in order of furthest from this species to closest) ornAna1 monDom4 mm9 rheMac2 panTro2 hg18

Check the following in the files:

- check annotated maf files for overlapping blocks: [hgwdev:/gbdb/ponAbe2/multiz8way/anno/maf> foreach f (*.maf)

      echo -n "${f}: "
      mafFilter -overlap -minRow=1 $f > /dev/null

end

If there are 'rejected blocks', contact the developer.

- Read both README files: /goldenPath/ponAbe2/phastCons8way/README.txt /goldenPath/ponAbe2/multiz8way/README.txt

- check upstream files to make sure that the species name doesn't appear in an "s" line: [hgwdev:~/goldenPath/ponAbe2/multiz8way/maf> zcat upstream*.maf.gz | grep "s ponAbe2" | wc -l 0 If this is not zero, contact the developer.

- check upstream files to make sure gene names haven't been truncated (to 9 chars): [hgwdev:~/goldenPath/ponAbe2/multiz8way/maf> zcat upstream*.maf.gz | head ##maf version=1 scoring=zero a score=0.000000 s NM_001017434 0 1000 + 1000 GTGAAGTGTCAGGGTGGAGAAGCAAATACAAACTCTTCACTAAGTGGCCCT If the gene names are short (9 characters) contact the developer.

- check one maf file: [hgwdev:~/goldenPath/ponAbe2/multiz8way/maf> zcat chrX.maf.gz | head

1. 1. maf version=1 scoring=autoMZ.v1

a score=21236.000000 s ponAbe2.chrX 2 249 + 156195299 cagtggcatgatcacagatgactgcagcctcggcctccatagc

Read through both description pages: Conservation track: - Check image that displays on conservation details page. - Check "Gene tracks used for codon translation" table against make doc. - Make sure organsisms are listed (in all places) in the correct phylogenetic order. - Make sure that this page includes all the extra sections (if the multizs have been anotated). - Make sure there is a tree model available.

Most Conserved track: - Make sure the text referrs to the correct species.

Check trackDb.ra file: Conservation track: - Make sure there is a speciesCodonDefault entry (usually is this species). - Make sure Jim has signed off on the species listed in the speciesDefaultOff entry.

Most Conserved track:

FIGURE OUT extFile AND seq: - if they are standard maf files, there will be no entries in the seq table. - There may be more than one set of entries in the extFile table. Make sure you only push the set that pertains to the actual files you are pushing to hgnfs1 (e.g. /gbdb/ponAbe2/multiz8way/anno/maf/*)

These are the ones that will need pushing to beta: mysql> select path from extFile where path like "%anno/maf%";

TO TEST IN BROWSER: - Zoom out past 1M bps (this tests the multiz*waySummary table) - Find example areas of all annotation types: pale yellow bar green square brackets vertical blue bar gaps

- Check out codon translation for a few species.

Tables Tests: - joinerCheck

- featureBits [hgwdev:~/qa/tracks/conservation/ponAbe2> nice featureBits ponAbe2 multiz8way gap -bed=output.bed 162920397 bases of 3093572278 (5.266%) in intersection

countPerChrom.csh ponAbe2 multiz8way

- find out how phastCons was run (from make doc). See if the species listed in the non-inf list make sense. In this case, they do not add to the phastCons wiggle. --not-informative