CHM13 unique Track Settings
 
CHM13 unique in comparison to GRCh38/hg38 and GRCh37/hg19   (All Mapping and Sequencing tracks)

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 CHM13 unique for hg38  CHM13 unique in comparison to GRCh38/hg38   Schema 
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 CHM13 unique for hg19  CHM13 unique in comparison to GRCh37/hg19   Schema 

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
    

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.