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I'm working on the same thing and here's what I've found: After importing Seurat object to Monocle, if you check: head(pData(imported_Seurat_object)), there should be a column of the clusters from...

@bishwaG pData() is in Monocle. Once you imported your Seurat object into Monocle, head(pData(Seurat object)) your Seurat clusters are in one of the columns.

@esfandyari Did you just import your Seurat object and run plot_cell_trajectory straight away? You need to go through steps like estimating size factors & dispersion, setting feature genes, reduceDimension(using Monocle's...

> > I'm working on the same thing and here's what I've found: > > After importing Seurat object to Monocle, if you check: head(pData(imported_Seurat_object)), there should be a column...

@Magdoll @chenzler I've seen duplicate multi-exon isoforms in the output, which like what you described before. These isoforms share identical internal junctions but number of exons do not match. This...

HI @Magdoll I tried using the latest Cupcake version v10.0.0, but still getting the same results. Here is the superPBID list: $ grep PB.1008 all_samples.chained_ids.txt superPBID sample1 sample2 PB.1008.1 PB.659.1...

Hi Liz @Magdoll One extra point I want to make. I've been using Ensembl annotation for this. I noticed that chain_samply.py doesn't work if GFF files in different samples do...

@cbravo93 same problem, have you fixed it?