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kharchenkolab / dropEst

Pipeline for initial analysis of droplet-based single-cell RNA-seq data
GNU General Public License v3.0
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10x V3 Chemistry #104

Open aelias1 opened 4 years ago

aelias1 commented 4 years ago

Unfortunately, DropEst is unable to work correctly with 10x V3. Should I simply use the new unfiltered barcodes for V3 and what other changes must be made?

aelias1 commented 4 years ago

I recently posted on github: I use the code below immediately following my loading in data - which is shown in your documentation:_cds <- preprocess_cds(_cds, num_dim = 100) _cds <- reduce_dimension(_cds) plot_cells(_cds)I receive the error: No trajectory to plot. Has learn_graph() been called yet? cluster not found in colData(cds), cells will not be colored cluster_cells() has not been called yet, can't color cells by clusterI cannot find in your Monocle 3 documentation these commands...at least to use before the commands stated above. I am using in data loaded from 10x the Response I received was that I should use learn graph first.  However, your documentation did no thave this and led me to use the code I used. Do you have updated documentation? Thank you. 

chlee-tabin commented 4 years ago

See this: https://github.com/hms-dbmi/dropEst/issues/105#issuecomment-641490931