Florencia1805
commented
4 years ago I actually also have another question. So I first did my QC steps in Monocle 2 before working with Monocle 3 as I believe Monocle 3 does not have the option to filter cells or genes (please correct me if I'm wrong). And I noticed that in the end, I have nicely filtered out my "bad" cells (similar amount as I had previously filtered out using Seurat), however, I still had the same amount of genes. Thus, these were not filtered. In the vignette it nicely shows the following function which I used in between my analysis:
expressed_genes <- row.names(subset(fData(eTregs), num_cells_expressed >= 3))
And this vector should now hold the identifiers for genes expressed in at least 3 cells of the dataset, but in the rest of the analysis it is more or less neglected. Thus, at the end I don't filter the genes out that I would actually like to filter out. Any idea how I can still do this?
Many thanks in advance, Florencia
jlilii
Hi,
Perhaps a very silly question, but I am very new to the field of scRNAseq analysis (and R in general). I am currently getting familiar with Monocle 3 after having worked with Seurat, mainly to be able to link my index sort files with my scRNAseq data.
Now I am also doing the rest of the analysis in Monocle as well, and have done clustering and differential gene expression analysis by using the vignette online (https://cole-trapnell-lab.github.io/monocle3/docs/differential/). However, I cannot seem to find anywhere how to export files with the DEGs per cluster... I have 5 clusters and am very curious to the lists of genes that are differentially higher expressed in those clusters compared to the other ones.
In Seurat, this was very straightforward to do, perhaps in Monocle as well but I have not managed to find out how.
Hope someone can help me out with this supposedly easy problem!
Kind regards, Florencia