1e8f4a189b1ad69e1cc4d60177b74ab1fd249da9
markd
  Fri Oct 2 22:22:36 2026 -0700
Record that previousPred has been deleted. refs #35528

367 GB of un-negated minus-strand predictions, kept while the negated files went
through QA. Deleting them loses nothing recoverable: negation is its own
inverse, so an original comes back by running proCapNetPredToFixedStep --negate
over the file now in pred/.

diff --git src/hg/makeDb/doc/hg38/transcriptionStart.txt src/hg/makeDb/doc/hg38/transcriptionStart.txt
index f731063c44b..5174803edd9 100644
--- src/hg/makeDb/doc/hg38/transcriptionStart.txt
+++ src/hg/makeDb/doc/hg38/transcriptionStart.txt
@@ -92,32 +92,34 @@
 # files were rewritten with negated values rather than rebuilt from the
 # downloads, which had already been deleted:
 #
 #   for db in hg38 hs1 ; do
 #       base=/hive/data/genomes/$db/bed/proCapNet
 #       mkdir -p $base/previousPred
 #       ls $base/pred/*.neg.bw | while read f ; do
 #           ~/kent/src/hg/makeDb/outside/proCapNet/proCapNetPredToFixedStep \
 #               --negate /hive/data/genomes/$db/chrom.sizes $f $base/negated/$(basename $f)
 #       done
 #   done
 #
 # Each output was checked against its input: same nBasesCovered, value range
 # mirrored, sampled values exactly negated.  The originals were then moved to
 # previousPred/ and the negated files put in their place, so /gbdb needs no new
-# symlinks.  previousPred/ is about 197 GB and can be removed once the track has
-# been through QA.  A rebuild from the downloads does not need any of this:
+# symlinks.  previousPred/ has since been deleted, 367 GB over the two
+# assemblies.  Nothing is lost by that: negation is its own inverse, so the
+# originals can be recovered from the files in pred/ by running the same command
+# again.  A rebuild from the downloads does not need any of this either:
 # proCapNetPredBuild negates the minus strand itself.
 
 ##############################################################################
 # ENCODE 4 PRO-cap
 ##############################################################################
 
 mkdir -p /hive/data/genomes/hg38/bed/encode4ProCap
 cd /hive/data/genomes/hg38/bed/encode4ProCap
 
 # Resolve the portal metadata: for each of the six experiments take only the
 # plus and minus strand signal of unique reads files belonging to that
 # experiment's default analysis, which drops files superseded by a later
 # reprocessing.
 ~/kent/src/hg/makeDb/outside/proCapNet/proCapNetEncodeMeta \
     ~/kent/src/hg/makeDb/outside/proCapNet/proCapNetExperiments.tsv encodeFiles.tsv