d93c426ef1ad5fbb32b754408599eaf380a199e5
max
  Tue Apr 21 13:34:58 2026 -0700
choriCloneEnds: reorganize danRer11 CHORI BAC clone end placements as a superTrack, refs #35059

- Rename ncbiCloneEndsCH1073 to choriCloneEnds throughout (trackDb, HTML,
makeDoc, scripts dir, /hive and /gbdb layout). User-visible label is
now "CHORI Clones" since all three libraries (CH1073, CH73, CH211) are
CHORI/BACPAC BAC libraries; data source (NCBI Clone DB) is cited in
Methods.
- Wrap the existing CH1073 track in a choriCloneEnds superTrack and
add two new subtracks built from the parallel unique_concordant GFFs
at ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ :
CH73  (99,141 placements, 23 oversize)
CH211 (70,231 placements, 46 oversize)
CH1073 is rebuilt with the same pipeline (210,777 placements).
- Build all three bigBeds with -extraIndex=name and register
searchTable / searchType bigBed stanzas with searchIndex name on each
subtrack, so clone names (CH1073-100A1, CH73-1A1, CH211-1A1, ...)
resolve from the Genome Browser position box.
- Single shared HTML description page; Methods now links to the NCBI
FTP source and to the UCSC makeDoc and scripts dir on GitHub.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

diff --git src/hg/makeDb/doc/danRer11/choriCloneEnds.txt src/hg/makeDb/doc/danRer11/choriCloneEnds.txt
new file mode 100644
index 00000000000..23881b62686
--- /dev/null
+++ src/hg/makeDb/doc/danRer11/choriCloneEnds.txt
@@ -0,0 +1,36 @@
+# CHORI zebrafish BAC library clone end placements track, refs #35059
+# 2026-04-21 Claude max
+#
+# NCBI Clone DB publishes per-library "unique_concordant" placement GFFs
+# under https://ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/ ,
+# computed against GRCz11 (danRer11). We expose three CHORI libraries
+# (CH73, CH211, CH1073) as a superTrack on danRer11.
+
+mkdir -p /hive/data/genomes/danRer11/bed/choriCloneEnds
+cd    /hive/data/genomes/danRer11/bed/choriCloneEnds
+
+# One-time: NCBI assembly report (col 7 RefSeq acc -> col 10 UCSC name).
+curl -sS -o GCF_000002035.6.assembly.txt \
+  'https://ftp.ncbi.nih.gov/genomes/all/GCF/000/002/035/GCF_000002035.6_GRCz11/GCF_000002035.6_GRCz11_assembly_report.txt'
+
+~/kent/src/hg/makeDb/scripts/choriCloneEnds/refSeqNames.py \
+    GCF_000002035.6.assembly.txt > refSeq.ucscName.tab
+# 1923 mappings, all names present in /hive/data/genomes/danRer11/chrom.sizes
+
+# Build each library with the same converter + autoSql. The name column
+# is indexed (-extraIndex=name) so clone names like CH1073-100A1 resolve
+# from the browser position box via "searchIndex name" in the trackDb.
+for LIB in CH1073 CH73 CH211; do
+    mkdir -p $LIB && cd $LIB
+    curl -sS -o $LIB.unique_concordant.gff \
+      https://ftp.ncbi.nih.gov/repository/clone/reports/Danio_rerio/$LIB.GCF_000002035.6.105.unique_concordant.gff
+    ~/kent/src/hg/makeDb/scripts/choriCloneEnds/makeBed.py \
+        ../refSeq.ucscName.tab /hive/data/genomes/danRer11/chrom.sizes \
+        $LIB.unique_concordant.gff > $LIB.bed 2> makeBed.log
+    sort -k1,1 -k2,2n $LIB.bed > $LIB.sorted.bed
+    bedToBigBed -extraIndex=name -type=bed6+7 \
+        -as=$HOME/kent/src/hg/makeDb/scripts/choriCloneEnds/cloneEnds.as \
+        -tab $LIB.sorted.bed /hive/data/genomes/danRer11/chrom.sizes $LIB.bb
+    cd ..
+done
+# clone_insert row counts: CH1073 210777, CH73 99141, CH211 70231.