ef779a5a2ed508cb00f0b0139a12d696e439ee5f
max
  Fri Sep 11 06:06:55 2026 -0700
new hg38 track hprcRdt: reference-divergent transcripts from 206 HPRC Release 2 genomes

Added as a third child of the existing long_read_transcripts superTrack,
alpha only for now. Data from Max Marin (DFCI), a bigPsl of RDT cluster
representative sequences aligned to GRCh38: 180,464 alignments of 120,451
distinct sequences from 412 haplotypes. Rebuilt from the submitted file only
to add a name index, refs #33822

diff --git src/hg/makeDb/trackDb/human/hg38/hprcRdt.ra src/hg/makeDb/trackDb/human/hg38/hprcRdt.ra
new file mode 100644
index 00000000000..3b35f4eaa15
--- /dev/null
+++ src/hg/makeDb/trackDb/human/hg38/hprcRdt.ra
@@ -0,0 +1,25 @@
+track hprcRdt
+superTrack long_read_transcripts
+shortLabel HPRC RDTs
+longLabel Reference-Divergent Transcripts from 206 HPRC Release 2 genomes (PacBio Kinnex)
+type bigPsl
+bigDataUrl /gbdb/$D/hprcRdt/hprcRdt.bb
+visibility pack
+searchIndex name
+indelDoubleInsert on
+indelQueryInsert on
+# above 200 kbp the alignments pile up too densely to read, so switch to a
+# coverage graph. The HLA and IGH loci carry tens of thousands of them.
+maxWindowCoverage 200000
+mouseOver <b>Transcript</b>: ${name}<br><b>Transcript length</b>: ${oChromSize} bp<br><b>Aligned bases</b>: ${match}
+
+# searchIndex on its own only tells hgFind which bigBed index to use. Without a
+# search spec stanza there is no hgFindSpec entry, and the transcript IDs are
+# not findable from the position box at all.
+searchTable hprcRdt
+# "bigBed" and not "bigPsl": hgFindSpec.c only skips the "does this MySQL table
+# exist" check for the literal string "bigBed", so any other big* value makes
+# the spec get dropped at load time for a track that has no table.
+searchType bigBed
+searchDescription HPRC reference-divergent transcript
+searchPriority 50