Ensembl Gene ID geneloc file for MAGMA?

[joeram]

Edit: This issue was kindly resolved by Masahiro Kanai - one can use the gene_annot_jun10.txt file with some reformatting as the MAGMA gene loc file.
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Hi,

I'm eager to try out PoPS, but I get the error "AssertionError: Covariate ids and Y ids don't match."

I imagine that this may be due to different gene ids (Entrez vs Ensembl). The authors of MAGMA provide links to gene location files with Entrez Gene IDs by default, whereas the example PoPS files seem to use ENSEMBL Gene IDs. I tried a manual conversion of Gene IDs before running MAGMA, but still end up with a slightly different list of genes and errors when running PoPS.

Is the gene location file (for MAGMA) used by the PoPS authors available somewhere?

Thanks!

[YaoChiehYao]

Hi joeram,

I am running with the same issue in step 2 of PoPs. I wrote a script to convert EntrezID into Ensembl ID in my out and raw file. (This part is fine) However, I cannot manage the data structure when I filter out genes that are not in the mouse brand tissue(in the gene_annot_jun10.txt file). Would you kindly share your solution?

Thanks

[JasonTan-code]

Do we know if the gene_annot_jun10.txt file is built on hg19 or hg38? I compared this file with NCBI37.3.gene.loc and NCBI38.gene.loc (provided by MAGMA) and found that this file does not match either.

By examining a few genes, gene_annot_jun10.txt appears to be more similar to NCBI37.3.gene.loc, but I believe they have different definitions of gene start and end locations.

[eightYao2]

@JasonTan-code
Hi Jason,
I’m also quite confused about whether the gene_annot_jun10.txt file is based on hg19 (GRCh37) or hg38 (GRCh38). Have you been able to confirm this?

[JasonTan-code]

I treat gene_annot_jun10.txt as hg19 build

[eightYao2]

@JasonTan-code
I sincerely appreciate your help.