LiftOver conversion

[Marina Murillo]

Hello,

I am using the LiftOver tool in order to convert genome coordinates from human T2T (hs1) to human hg38.

Multiple coordinates of the T2T genome coincide with the same coordinate of the hg38 genome.

For example:

                     T2T                                           hg38

chr1 160732018 160732088      chr1 161469399 161469470
chr1 160680275 160680345      chr1 161469399 161469470
chr1 160621248 160621318      chr1 161469399 161469470
chr1 160613855 160613925      chr1 161469399 161469470

The oposite can be found to, multiple coordinates of the hg38 genome coincide with the same coordinates of the hg38 genome.

                       hg38                                                     T2T

chr6 28953266 28953337                          chr6 28828036 28828108
chr6_GL000251v2_alt 439673 439744      chr6 28828036 28828108
chr6_GL000253v2_alt 218828 218899      chr6 28828036 28828108
chr6_GL000254v2_alt 219011 219082      chr6 28828036 28828108
chr6_GL000255v2_alt 218847 218918      chr6 28828036 28828108
chr6_GL000256v2_alt 262652 262723      chr6 28828036 28828108

What could be the explanation for this?

Thanks,

Marina.

--

Marina Murillo Recio

PhD Student

Gene Translation Laboratory

Institute for Research in Biomedicine (IRB Barcelona)

Baldiri Reixac, 10 - 08028 Barcelona, Spain 

Phone: +34 93 40 34867

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

The following help page should provide more information about these extra results.

https://genome.ucsc.edu/FAQ/FAQblat.html#blat1c

hg38 has had patches and fixes to the genome to resolve issues. These issues may be resolved in a newer assembly, such as T2T, and can result in additional hits. More information about patches can be found on the Genome Browser blog:

https://genome-blog.soe.ucsc.edu/blog/2019/02/22/patches/

Going to the following region on T2T (chr1:160,613,856-160,732,088), a large portion of this region is unique to T2T compared to hg38:

https://genome.ucsc.edu/s/jnavarr5/hs1.MLQ_30580

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro

UCSC Genome Browser

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