Description

These tracks show the regions unique to the T2T-CHM13 v2.0 assembly compared to the GRCh38/hg38 and GRCh37/hg19 reference assemblies.

Methods

Converting a chain file to the PAF format

We used the `to_paf.py` script from chaintools (https://doi.org/10.5281/zenodo.6342391, v0.1) to convert the v1_nfLO chains to the PAF format.

Obtaining unique regions

We used the follwing commands to obtain the regions unique to GRCh38/hg38 and GRCh37/hg19 in the BED format.

cut -f 1,3,4 grch38-chm13v2.paf  \
  | bedtools sort -i - -g chm13v2.0.fasta.fai \
  | bedtools merge \
  | bedtools complement -g chm13v2.0.fasta.fai -i - \
  | bedtools merge \
  > T2T-CHM13v2.0_unique_regions_hg38.bed

cut -f 1,3,4 hg19-chm13v2.paf |  bedtools sort -i - -g chm13v2.0.fasta.fai \
  | bedtools merge \
  | bedtools complement -g chm13v2.0.fasta.fai -i - \
  | bedtools merge \
  > T2T-CHM13v2.0_unique__regions_hg19.bed

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can also be accessed from scripts through our REST API.

This track is a container of multiple subtracks; the underlying data are stored in bigBed files that can be downloaded from our download server. 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 only features within a given range, for example:

Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Credits

The unique region annotations were generated by Nae-Chyun Chen<naechyun.chen@gmail.com> and Mitchell Vollger<mvollger@uw.edu>

References

Nurk S, Koren S, Rhie A, Rautiainen M, et al. The complete sequence of a human genome. bioRxiv, 2021.