+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. +