T2T fixed GRCg38 gaps and issues, gaps genomic coordinates.

Question

[marinamrbiotech]

Hello everyone,

I want to know the coordinates in T2T for the fixed GRCh38 gaps. The exact coordinates that I am looking for are represented in figure A, regions marked in black. Where can I find the information for those coordinates ?

Thanks,
Marina.

[biofalconch]

I guess you can try and "Lift" the coordinates from one assembly to the other. But you need to get a BED file for those regions. :)

https://genome.ucsc.edu/cgi-bin/hgLiftOver

[marinamrbiotech]

Thanks for your answer. The bed file with the T2T coordinates is what I want. If then I need to know the coordinates for hg38 I could us LiftOver as you suggested :)

[Matthias Zepper]

Can't you just align the two references against each other? A quick Google search turned up e.g. GSAlign or Cactus, which - on the first glance - seem to be suited for this task?

[marinamrbiotech]

Yes this could be an option, but I thought that maybe I could find the info in a database, in order to don't waste time running the aligments :)

Answer 1

[DBScan]

If you want to know the regions which are new in T2T compared to hg38/hg19, you can use this 2T.UCSC.hgUnique.hg38. Also accessible via AnnotationHub under "AH107353".

[marinamrbiotech]

Hi, thanks for your answer it was very useful. The file that I can obtain from the link that you attached is binary BigBed format. How can I convert the BigBed format to a simple bed file.

Thanks :)

[biofalconch]

From the tools provided by UCSC (you can find pre-compiled binaries for linux here: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/) there is a specific tool for this called bigBedToBed

[DBScan]

You can download from the Google Drive link provided by Mikhail Dozmorov: T2T.UCSC.hgUnique.hg38

[Ram]

Care to show us where Mikhail themselves shared this link? Owing to the suspicious nature of the link, the spambot automatically flagged your comment. I examined the link and removed this flag.

[DBScan]

On the Github site from excluderanges Github Exluderanges, "New (2022-09-20) - Exclusion sets for human T2T-CHM13 and mouse GRCm39/mm39 genome assemblies are available. Download all data from Google Drive."

[Ram]

The right way to do this would have been to point to the GitHub page and mention the Google Drive link so people can get the full context. Mikhail Dozmorov is probably not well known to everyone so pointing to the GitHub page adds credibility to the link or at least some sort of backing that it's not a malicious link. Always point to as close as you get to the primary source.

[marinamrbiotech]

Thank you very much !! This is what I needed. So the file in 2T.UCSC.hgUnique.hg38 --> /gbdb/hs1/hgUnique/hgUnique.hg38.bb is the same as in T2T.UCSC.hgUnique.hg38.bed, the only difference is the file format ?