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T2T-CHM13 "complete" human genome gff/gtf annotation file

Hi all,

There is a great preprint for the "complete" human genome T2T-CHM13 on bioRxiv. I'm not able to find a gff/gtf/bed annotation file for this and I was hoping someone might share a link if one exists.

https://www.biorxiv.org/content/10.1101/2021.05.26.445798v1.full

https://github.com/marbl/CHM13

Thanks!

genomics
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updated by usa.cd.genomics • usa.cd.genomics • written by noodle noodle

4 answers

NCBI has T2T assembly. FTP site for the sequence and annotation files : https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/

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written by GenoMax GenoMax

Hey, it looks like the correct link is now on Github.

See https://github.com/marbl/CHM13#downloads.

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written by kojix2 kojix2

Hey thanks, I see they uploaded a GFF for v1.1 to the github page now.

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written by noodle noodle

I'm not able to find a gff/gtf/bed annotation file for this

the annotations are available as bigbed/bigwig in the ucsc hub: http://t2t.gi.ucsc.edu/chm13/hub/t2tChm13_20200727/

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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you Pierre, can you point me to a bb/bw file with gene/transcript annotations? Does this exist (I can't find for v1.1, where they have accurate rRNA/rDNA annotations)?

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written by noodle noodle

keep in mind you may have difficulty finding a gaps.txt file ... in perpetuity

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written by LauferVA LauferVA

Maybe you can see this:epigenetic modification

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written by usa.cd.genomics • usa.cd.genomics

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