8faeb3cba60c7cb842bc17c17a57c9b53ef1b478
max
  Tue Apr 21 02:51:32 2026 -0700
ncbiCloneEndsCH1073: add NCBI CH1073 BAC library clone end placements track on danRer11, refs #35059

210,777 unique-concordant clone-insert placements from NCBI's CH1073
(RZPD-1073 / DanioKey) library clone report. Separate from the existing
bacEndPairsLift (danRer4 -> danRer11 UCSC-BLAT lift), which is left in place.

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

diff --git src/hg/makeDb/doc/danRer11/ncbiCloneEndsCH1073.txt src/hg/makeDb/doc/danRer11/ncbiCloneEndsCH1073.txt
new file mode 100644
index 00000000000..a8631027908
--- /dev/null
+++ src/hg/makeDb/doc/danRer11/ncbiCloneEndsCH1073.txt
@@ -0,0 +1,34 @@
+# NCBI CH1073 clone end placements track, refs #35059
+# 2026-04-21 Claude max
+
+mkdir -p /hive/data/genomes/danRer11/bed/ncbiCloneEndsCH1073
+cd /hive/data/genomes/danRer11/bed/ncbiCloneEndsCH1073
+
+# NCBI assembly report (has the UCSC-style name in column 10, so we just
+# project col 7 (RefSeq accession) onto col 10 (UCSC name))
+curl -sS -o GCF_000002035.6.assembly.txt \
+  'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/035/GCF_000002035.6_GRCz11/GCF_000002035.6_GRCz11_assembly_report.txt'
+
+# CH1073 unique_concordant placements (210777 clone_insert rows, ~48 MB)
+curl -sS -o CH1073.unique_concordant.gff \
+  'https://ftp.ncbi.nlm.nih.gov/repository/clone/reports/Danio_rerio/CH1073.GCF_000002035.6.105.unique_concordant.gff'
+
+# RefSeq acc -> UCSC chrom name
+~/kent/src/hg/makeDb/scripts/ncbiCloneEndsCH1073/refSeqNames.py \
+    GCF_000002035.6.assembly.txt > refSeq.ucscName.tab
+# 1923 mappings, all names present in /hive/data/genomes/danRer11/chrom.sizes
+
+# Parse GFF -> BED 6+7 (matches cloneEnds.as). All 210777 clone_insert rows
+# map to UCSC names; 26 are flagged as oversize (insertSize > 500 kb).
+~/kent/src/hg/makeDb/scripts/ncbiCloneEndsCH1073/makeBed.py \
+    refSeq.ucscName.tab /hive/data/genomes/danRer11/chrom.sizes \
+    CH1073.unique_concordant.gff \
+    > ncbiCloneEndsCH1073.bed 2> makeBed.log
+
+# Sort and convert to bigBed
+sort -k1,1 -k2,2n ncbiCloneEndsCH1073.bed > ncbiCloneEndsCH1073.sorted.bed
+bedToBigBed -type=bed6+7 \
+    -as=~/kent/src/hg/makeDb/scripts/ncbiCloneEndsCH1073/cloneEnds.as \
+    -tab ncbiCloneEndsCH1073.sorted.bed \
+    /hive/data/genomes/danRer11/chrom.sizes \
+    danRer11.ncbiCloneEndsCH1073.bb