T2T-CHM13 "complete" human genome gff/gtf annotation file
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3 months ago
joe ▴ 230

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 • 1.2k views
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5 weeks ago
kojix2 ▴ 180

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

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

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

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3 months ago

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

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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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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/

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A track showing gene models as from liftoff based on GENCODE

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

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