Could you add T2Tv2.0 new assembly (so called Hs1) to hg19 and hg38? Thanks

[josegarciamanteiga]

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[bschilder]

Hi @josegarciamanteiga , would you mind giving us a bit more info on this?

Namely:

• Where can we find this assembly?
• At which steps do you want this to be used?
• Is there currently a Bioconductor package that distributes this package? We rely on these reference genome packages for EpiCompare. For example, BSgenome.Hsapiens.UCSC.hg19

Thanks,
Brian

[josegarciamanteiga]

Hi! Yes, that's right. It's a complex thing and we might have to wait until bioc people puts it in Bioc standard annotation packages. All the annotation of T2T (hs1) most updated I found it here: https://github.com/marbl/CHM13 As you can see, there are already liftOvers to some ENCODE trancks, but you could use your own liftOver functions using the hs1.to.hg38 chain, if you want. But I think it should be better to liftOver ENCODE to hs1 and keep everything in the new genome. The only BioC package I know is here: https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0.html But I think it is just the fasta of the genome, so if you can't do it without Hsapiens.UCSC.hs1, then I think I'll wait. Thanks anyway for a great package! Jose

…

-------------------------------------- Jose M. Garcia Manteiga PhD Computational Biologist Center for Translational Genomics and BioInformatics Dibit2-Basilica, 4A3 San Raffaele Scientific Institute Via Olgettina 58, 20132 Milano (MI), Italy Tel: +39-02-2643-9211 e-mail: ***@***.*** Il giorno mar 14 feb 2023 alle ore 18:50 Brian M. Schilder < ***@***.***> ha scritto:

Hi @josegarciamanteiga <https://github.com/josegarciamanteiga> , would you mind giving us a bit more info on this? Namely: - Where can we find this assembly? - At which steps do you want this to be used? - Is there currently a Bioconductor package that distributes this package? We rely on these reference genome packages for EpiCompare. For example, BSgenome.Hsapiens.UCSC.hg19 <https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html> Thanks, Brian — Reply to this email directly, view it on GitHub <#137 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA2UOMOHCCJREW2FOFCXPY3WXPAYFANCNFSM6AAAAAAUX5F424> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[bschilder]

Thanks for the helpful info, @josegarciamanteiga ! We will look into this further and see to what extent we can incorporate in regards to EpiCompare. If possible, would be great to have. We'll keep you posted here as things develop.

Best,
Brian