This track is part of the Long-read Transcripts collection.
It shows reference-divergent transcripts (RDTs) found in the genomes of the Human Pangenome Reference Consortium (HPRC), aligned back onto GRCh38. An RDT is a transcript that was sequenced and assembled in one of these genomes but that does not match the GRCh38 gene annotation well, either because it uses splice sites or exons that the reference annotation does not have, or because it comes from a region where the donor genome differs from the reference. Transcripts like these are invisible to an analysis that maps reads only against GRCh38, so they are one way of measuring how much of human transcript diversity a single reference genome misses.
The track holds about 180,000 alignments of roughly 120,000 distinct transcript sequences, drawn from 412 haplotype assemblies of 206 individuals. Alignments are far from evenly spread. Around 40% of them fall in two places: the MHC class I region on chr6 and the immunoglobulin heavy chain locus on chr14. Both are among the most polymorphic loci in the genome, so a reference-based annotation is expected to describe them poorly.
Each item is the alignment of one transcript sequence to GRCh38. Blocks are aligned segments, thin connecting lines with arrows are the gaps between them, and the arrows give the strand the transcript aligns to. Because these are alignments rather than gene models, the display also marks where the transcript and the reference disagree: an orange line marks bases that the transcript has in the middle of the alignment but the reference does not, a purple line marks the same at either end of the transcript, and a pair of horizontal lines marks a place where both sequences have an insertion relative to the other. These markers can be turned off in the track configuration.
The item name is the identifier of the transcript in its source haplotype, so it carries the sample name, the haplotype, and the PacBio locus and isoform number, for example G_PBKT.HG01960_Hap1_PB.104.1. Names can be typed into the position box to jump to a transcript. The same transcript can align in more than one place, so a name can match several positions and the position box then offers a list.
Where the alignments are too dense to tell apart, the track switches by itself to a coverage graph. In the most crowded parts of the MHC this happens in a window of only a few kilobases; elsewhere it happens once the window passes 200 kbp.
Full-length RNA of 206 HPRC Release 2 samples was sequenced with the PacBio Kinnex protocol. For each sample, transcripts were assembled and annotated against that sample's own two haplotype assemblies rather than against GRCh38, giving 412 per-haplotype transcript annotations. Each transcript was compared to the reference annotation lifted onto the haplotype with Liftoff and classified with gffcompare, and coding potential was assessed with ORFanage. Transcripts that diverged from the reference annotation were kept as RDTs. The RDT sequences from all haplotypes were then clustered at 99% sequence identity and 99% coverage, and one representative sequence per cluster was aligned back to GRCh38 to produce this track. The per-haplotype annotations themselves, which carry the gene assignment, gffcompare class code, read support and ORF calls for every transcript, are available as a track hub on the individual HPRC assemblies (see the repository linked below).
The alignment file was downloaded from https://github.com/maxgmarin/hprc-r2-rdt-testhub, file Data/HPRC.PanTx.ClusteredRDTsRepSeqs.SID99C99.AlnToHG38.bb. At UCSC it was converted back to text, checked against the GRCh38 chromosome sizes, and rebuilt as a bigBed with an index on the transcript name so that names can be searched. No alignments were added or dropped: the 180,464 alignments in the source file are all present in the track. Note that the source file records no mismatch counts, so the per-alignment details page reports every alignment as 100% identity regardless of how much the transcript actually diverges from GRCh38. The commands used are in the makeDoc, and the build script is in the kent source tree.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-sep tables. From scripts, the data can be accessed through our API, track=hprcRdt.
For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called hprcRdt.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/hprcRdt/hprcRdt.bb -chrom=chr21 -start=0 -end=100000000 stdout
The original annotation source data can be downloaded from https://github.com/maxgmarin/hprc-r2-rdt-testhub.
Thanks to Max Marin at the Dana-Farber Cancer Institute for producing this annotation and making it available, and to the Human Pangenome Reference Consortium for the assemblies and the sequencing data.