I don't know if this is an appropriate question here, but I am lost. Is here someone with RStudio and scRNA-Seq experience, who is willing to help me with my project? Maybe talking via Discord? (I am living in the time zone Europe/Berlin.)
I took this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8077299/ and need to re-do the analysis of the scRNA-Seq parts, but after quite a few hours I got a complete different UMAP (there is no similarity between the paper and mine) and the search for marker genes, which should give me markers for the enterocytes, stem cells, etc,- resulted surprisingly in cancer cells.
Furthermore, I honestly do not know how to proceed with the TAP-count matrix.
I asked the authors for their script, but I am not sure if they are going to help me. That's why I am asking here.
I know that I will not recreate exactly the same UMAP, but I thought there should be some similar structures.
I let R giving me the top MarkerGenes for each clutster and I searched quickly their names on Google. And every MarkerGene was associated with an GI cancer.
So, I took their already with cell ranger processed files to save some time and I think I did every step they have mentioned in the method part. In my bioinformatics course we had a short introduction to Seurat, so I also orientated on this.
Well, it's not surprising some markers will be associated with GI cancers given that it's GI tissue. Just because a gene is associated with cancer (though what gene isn't, at this point), that doesn't mean it can't be used as a cell-type marker as well. Did you look at the markers they show in figure 1? I expect those will help you annotate your clusters to match theirs.
Ok I will try it sometime later. Thanks for your input.