fjrossello

Hi, As far as I can see in the screenshot attached, `--start-trim` should equal 10 as in `--start-trim 10` since your tag sequence starts at the 11th base.

Hi, I get the same error using both `v1.4.5` (`Python 3.8`) and `v1.4.3` (`Python 3.6.5`). I am trying to process a `TotalSeqC` experiment using 4 tags with a total of...

Hi, Thanks for your prompt reply. I have just run it using `-n 20000000` and `-n 2000000` combined with `-T 16` and `T 32` and got the same output. Please...

Hi, Thanks for your prompt reply. As advised, I tried using hardcoded paths in the script without success. I have also tried by including all necessary files within the same...

Hi, Sorry, I am not sure what you mean by _from the command line directly_. Thanks for your help. Cheers,

Thanks for clarifying. I did run the last two examples re hardcoded paths from the command line. As I mentioned, still the same output. Thanks again for your help. Cheers,

An update. The origin of my issue was having a mixture of read lengths in `R2` (from `8` to `25` bases, `0.01%` of the total no. of reads) which caused...

Adding to the solution posted by @jgarces02, the `find_genes_modules` function requires pre-calculated gene/feature loadings (`PCA/LSI`, more here #191). If imported from a `Seurat` object and using `PCA`, gene loadings should...

As previously mentioned, I used mostly what described by @jgarces02 and [here](https://github.com/cole-trapnell-lab/monocle-release/issues/388#issuecomment-652537985) with the modifications described in my comment. I have use the `SeuratWrapper` function `as.cell_data_set` using the `default.reduction` of...