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

Question

[noodle]

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!

Answer 1

[GenoMax]

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/

Answer 2

[kojix2]

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

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

[noodle]

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

Answer 3

[Pierre Lindenbaum]

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/

[yech1990]

There are still no annotation files for the latest version. http://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v1.1/

[LauferVA]

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

[noodle]

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)?

[Pierre Lindenbaum]

This track contains RefSeq Gene alignments produced by the TransMap cross-species alignment algorithm from other human GRCh38.

http://t2t.gi.ucsc.edu/chm13/hub/t2tChm13_20200727/transMap/

[Pierre Lindenbaum]

A track showing gene models as from liftoff based on GENCODE

http://t2t.gi.ucsc.edu/chm13/hub/t2tChm13_20200727/liftOffGenes/