e6d1189bea4cc541396f842b65a3392c33c8e734
max
Wed Sep 2 02:55:03 2026 -0700
hprc2annot: put the collection in git and fix the QA findings
The HPRC Release 2 GenArk contributed track collection (7 tracks x 462
assemblies) had only its one-line betaGenArk.txt enable checked in. Add the
makeDoc, the build scripts, the seven track description pages and the trackDb
stanzas, and fix the problems QA found.
Data fixes, both rebuilt across all 462 assemblies:
- liftoff: gff3ToGenePred was naming each genePred after the gene, so every
transcript of a gene shared one name, the RefSeq accession was lost and the
transcript_biotype lookup never matched (type empty on 99.8% of rows). Pass
-rnaNameAttr=ID. Duplicate (chrom,start,end,name) tuples go from 24,969 to 0
and type is now empty on 2,132 of 82,973,730 rows. The same flag is a no-op
on the CAT GFF3 (byte-identical output), so both gene tracks now share one
code path and CAT needs no rebuild.
- segdups: the build read SEDEF column 6, strand1, which is "+" by construction
on every row, so every inverted duplication rendered forward. Use column 14,
strand2, the orientation of the paralogous copy: 13.8M + and 13.8M - across
the collection. Also translate the paralog partner out of PanSN through the
GenArk chromAlias, since the browser does not translate a plain text field,
and store identity as a percentage so the mouseover can read it.
hprc2annotFixBed.sh is not idempotent for pclai: a second run re-parses an
already-parsed name and blanks the values. It now refuses to touch a converted
file. GCA_041900255.1 was damaged that way and is rebuilt from source.
Provenance, all from the QA report:
- stats.tsv is appended to rather than truncated on every run, and each run
regenerates log/summary.tsv, a per-track roll-up over the collection.
- dataVersion on all seven tracks.
- Rows are now dropped for exactly two reasons and both are counted: past the
end of the sequence, or a sequence name absent from the assembly, which also
warns with example names. Only GCA_018472765.3 trips the second, the known
upstream contig-version mismatch. genePredToBigGenePred failure is checked
and an empty conversion result is a failure, not a valid empty bigBed.
Description pages: fix a raw UTF-8 character, rewrite the segdups and pclai
display conventions which still described the data before the name field was
blanked, add a color legend checked against the data, add the pcLAI preprint
(from the Crossref record, since it has no PMID), and correct the stated reason
liftoff drops transcripts.
Display: title case on the short labels, "Active centromeres" shortened to fit
the 17-character limit, pcLAI to pack since it has no readable dense state,
liftoff and segdups to dense, and a filter on the segdups original flag.
refs #35415
diff --git src/hg/makeDb/trackDb/contrib/hprc2annot/censat.html src/hg/makeDb/trackDb/contrib/hprc2annot/censat.html
new file mode 100644
index 00000000000..599bff30b54
--- /dev/null
+++ src/hg/makeDb/trackDb/contrib/hprc2annot/censat.html
@@ -0,0 +1,71 @@
+Description
+
+This track shows the centromere satellite (cenSat) annotation for this Human
+Pangenome Reference Consortium (HPRC) Release 2 assembly. Centromeres and other
+heterochromatic regions of human chromosomes are built largely from
+satellite DNA: long stretches of short sequences repeated head to tail
+millions of times. These regions are where the cell's machinery attaches during
+cell division, and until complete (telomere-to-telomere) assemblies became
+available they could not be sequenced or annotated. This track labels the
+different families of satellite repeat along each sequence, including the alpha
+satellite higher-order repeats that define the active centromere.
+
+
+Display Conventions
+
+Each item is one satellite region, labeled with its repeat class (for example
+alpha-satellite higher-order repeat, monomeric alpha satellite, or one of the
+human satellite families HSat1/2/3). Items are colored by the standard cenSat
+annotation color scheme, so that the different satellite families can be told
+apart at a glance; the specific family is given in the item name and on the
+details page. The repeat-class name is searchable.
+
+
+Methods
+
+The cenSat annotation identifies and classifies satellite arrays in a complete
+assembly, combining alpha-satellite higher-order-repeat detection with a
+repeat-family classification of the remaining satellite sequence, following the
+approach developed for the telomere-to-telomere CHM13 reference (see reference
+below).
+
+
+The annotation files were obtained from the HPRC Release 2 data collection on the
+public s3://human-pangenomics bucket, indexed at
+the hprc_intermediate_assembly data tables.
+Each per-assembly cenSat BED file was converted to a UCSC bigBed file, preserving
+the item colors. The steps are described in the
+makeDoc,
+the build scripts are in the
+kent source tree,
+and the track configuration is in
+trackDb/contrib/hprc2annot.
+
+
+Data Access
+
+For automated analysis, the annotation is stored in a bigBed-format file
+(censat.bb) that can be read with the UCSC tool bigBedToBed,
+which can be compiled from source or downloaded as a precompiled binary. The
+original annotation files are available from the HPRC S3 bucket linked above.
+
+
+Credits
+
+Annotations were generated by the Human Pangenome Reference Consortium. Thanks to
+the HPRC production team for making these data available.
+
+
+References
+
+
+
+Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov
+FD, Shew CJ et al.
+
+Complete genomic and epigenetic maps of human centromeres.
+Science. 2022 Apr;376(6588):eabl4178.
+PMID: 35357911; PMC: PMC9233505
+
+