David

Hello there I'm having the same initial problem than Kevin. I'm running : (base) david@Dalhte:/media/david/E/finder_v1.1.0$ run_finder --metadatafile $PWD/Rattus_metadata5.csv --output_directory $PWD/FINDER_test_Rattus --genome $PWD/Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa --organism_model VERT --genemark_path $PWD/gmes_linux_64 --genemark_license $PWD/gm_key_64 --cpu 5...

Hello again I solved part of my problem modifying the concat parameters to : >>> adata_atacPG = adata_atacPG2.concatenate([adata_atacPG6, adata_atacPG24, adata_atacPG13], join='outer') And retrieved 3000 more genes. But, I'm quite greedy...

me again, realizing my last question was discussed in previous #29 and #1 post !

Hi there I still have some problems I cannot solve this time : In my RNA anndata object (adatam1), I have 13873 genes In my ATAC anndata object ( adata_atacPGc),...

Hi again I tried several things randomly: it seems that "getAssaData" is deprecated in Seurat5 and to be replaced with LayerData, so could my problem come from incompatibility between Seurat5...

If ever it can help someone, here is what I did : I bypassaded the getassayy using layerdata function: objG[['SoupXRNA']]

Hi @lzj1769 Don't worry, it was nice to find a solution by myself :) Even if the solution is quite tedious :DDD Best David

> Hello @liyang24 I am not a specialist but here is what I did to implement the rat genome (rn6) #### create a gene annotation for RN6 #get the library...

> Hi! I was running into an issue when selecting TFs in my mouse data, because the motif names did not match many genes in the gene exp data. I...

Hi Amanda Thanks a lot ! It's working :) Just to know, did you had incompatibility problems between ScMEGA and seurat V5 (if you use seurat that is ?) I...