25cb79b4a110974de7622bc22f4970dbd9cf36b6
markd
  Tue May 4 18:36:51 2021 -0700
added instructions for making transMap QA data

diff --git src/hg/makeDb/doc/transMapTracks.txt src/hg/makeDb/doc/transMapTracks.txt
index 416d04d..557155c 100644
--- src/hg/makeDb/doc/transMapTracks.txt
+++ src/hg/makeDb/doc/transMapTracks.txt
@@ -156,23 +156,29 @@
   (cd ../V5/stats/detailed && find -type f)  | sort >V5.stats.lst
   (cd ../V6/stats/detailed && find -type f)  | sort >V6.stats.lst
   diff V5.stats.lst V6.stats.lst >&stats.lst.diff
 
   # all removed genomes have been deactivated as they have been moved to
   # assembly hubs.  these are not public hubs.
 
   # create symlinks to /gbdb for bigPsl files
     ${tmdir}/bin/linkToGbdb  ${tmdir}/etc/transMapBuildConf.py
 
   # add trackDb entries at top level by editing:
     src/hg/makeDb/trackDb/trackDb.transMap.ra 
   # create push lists for databases and gbdb files for genomes on hgwbeta:
     ${tmdir}/bin/mkPushList ${tmdir}/etc/transMapBuildConf.py db.push.lst gbdb.push.lst
 
+   # make collect QC data and plots
+   ${tmdir}/bin/transMapStatsQCPlot --countChangeTsv=transMap-V5-V6.stats.tsv ../V5/stats/overall.stats.tsv ../V5/db.push.lst stats/overall.stats.tsv db.push.lst transMap-V5-V6.stats.pdf
+   ${tmdir}/bin/transMapDetailsCmp ../V5/stats/detailed stats/detailed transMap-V5-V6.detailed.tsv
+
   # update tracks
   # add  transMapV6.html
   # update  trackDb.transMap.ra
 
   cd src/hg/makeDb/trackDb
   make -j 64
 
+
+
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