This track is part of the Methylation and 3D Chromatin collection of the zebra finch telomere-to-telomere hub.
This track is the interval form of the Hi-C compartment call: the same 200 kb analysis as the Compartment E1 track, reduced to labelled A and B blocks. It is the easier of the two to read when zoomed out, and the easier one to intersect with other annotations. It contains about 3,100 intervals.
Intervals are colored by compartment.
| A compartment, open and gene rich | |
| B compartment, closed and heterochromatic |
Produced by the same cooltools eigs-cis analysis as the Compartment E1 track, with the sign of the first eigenvector at 200 kb converted into A and B interval calls. Topologically associating domain boundaries were also computed at 200 kb with cooltools insulation, and are not part of this hub.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/3D/bTaeGut7v0.4_MT_rDNA.Cooltools.E1.200kbp.flipped.dip.collated.v0.1.bed. It is a text format that a track hub cannot use directly, so it was converted to a binary indexed file. The conversion, and the whole hub, is reproduced by the commands in src/hg/makeDb/doc/contrib/bTaeGut7.txt of the UCSC 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-separated tables. From scripts, the data can be accessed through our API, track=compartAB.
For automated download and analysis, this annotation is a bigBed file inside the hub. Individual regions or the whole annotation can be obtained with bigBedToBed, which can be compiled from source or downloaded as a precompiled binary; instructions are here. The tool also fetches a range, for example bigBedToBed <hubUrl>/GCF_048771995.1/compartAB.bb -chrom=NC_133024.1 -start=0 -end=100000 stdout, where <hubUrl> is the directory this hub was loaded from.
The original annotation files are on GenomeArk, in the bTaeGut7 annotations directory.
Formenti G, Jain N, Medico JA, Sollitto M, Antipov D, Barcellos S, Biegler M, Borges I, Chang JK, Chen Y et al. The complete genome of a songbird. Cell. 2026 Aug 6;189(16):4922-4945.e12. PMID: 42561917
Open2C, Abdennur N, Abraham S, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Oksuz BA, Venev SV et al. Cooltools: Enabling high-resolution Hi-C analysis in Python. PLoS Comput Biol. 2024 May;20(5):e1012067. PMID: 38709825; PMC: PMC11098495
The assembly and all of these annotations were produced by the Vertebrate Genome Laboratory at The Rockefeller University and their collaborators, and released through GenomeArk. Thanks to Giulio Formenti and Erich D. Jarvis and their co-authors for making the data available before and after publication. The analysis code is at github.com/gf777/T2T-zebra-finch. This hub was assembled at UCSC from the IGV session distributed with the annotations, using hubtools.