Question related to build GRCh38

[bmateosa]

Hello,
Thank you for providing gsMap, I am really enjoying using this excellent resource.
I have a question regarding genome builds. For Visium HD spatial transcriptomics processed with Space Ranger, 10X provides the reference "refdata-gex-GRCh38-2020-A" which I am using for my ST samples. However, the GWAS summary statistics I integrate with gsMap are in GRCh37.

Could you please advise whether using different genome builds for ST data and GWAS could cause issues in gsMap? If so, would you recommend converting the GWAS to GRCh38 (or another approach) before running the analyses?

Thank you very much in advance.

[LeonSong1995]

Hi,

I am glad to hear that you enjoy using gsMap. It is fine to use ST data processed with GRCh38, as the gene names in GRCh38 and GRCh37 are nearly identical. In gsMap, GWAS SNPs are mapped to genes based on the GTF annotation, so consistency between the genome version of the GTF file and the reference LD panel is what matters. As long as these two use the same genome build, everything will work correctly.

Best,
Liyang