Liftover RN7 to RN8 Doesn't Working

[Yixuan Xin]

Hello UCSC liftover team,

My name is Ivy and I’m in Palmer lab UCSD trying to do the Liftover on rats microarray data from Rn5 to Rn8, but the only available version are from Rn5 to Rn7 and Rn7 to Rn8. I saw in this link: https://hgdownload.soe.ucsc.edu/goldenPath/rn7/liftOver/ there is a new chain file being published on 08.11.25 called rn7ToGCF_036323735.1.over.chain.gz, is this the correct chain file from Rn7 to Rn8? Or Where can I find it? For this file I have trouble load it in R, but I can open/import other chain files successfully, so I’m guessing the issue is because it contains NCBI ids. The headers are like this: 

chain 24420673074 chr1 260522016 + 7552 260522016 NC_086019.1 270518180 + 71937 270508008 1

But that’s only my guess. Could you help me find a way to load it? Thank you!

Best,

Ivy

[Luis Nassar]

Hi, Ivy.

We've gone ahead and generated the chain file directly from rn5 to rn8. We are using NCBI RefSeq (GCF) or GenBank (GCA) identifiers for most of our new assemblies now, so rn8 is GCF_036323735.1, like you say.

https://hgdownload.soe.ucsc.edu/goldenPath/rn5/liftOver/rn5ToGCF_036323735.1.over.chain.gz

We're not familiar with how you are importing it to R (rttracklayer?), but if the rn8 assembly has UCSC-style chromosome names (e.g., chr1, chr2), then you will need to convert those over in the chain file. We provide an alias file for rn8 there:

https://hgdownload.soe.ucsc.edu/hubs/GCF/036/323/735/GCF_036323735.1/GCF_036323735.1.chromAlias.txt

From there, you would convert from the items in the RefSeq column (e.g., NC_086019.1), probably to Assembly or UCSC, depending on what you are working with (e.g., chr1).

Let us know if you need help with anything else or additional clarifying steps.

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Lou Nassar
UCSC Genomics Institute