Gioele La Manno
Gioele La Manno
I am not sure what is happening, maybe cell ranger changed output folder structure? I haven't looked into that recently. Maybe there are many barcodeless reads at the beginning of...
We are looking into that there could be a problem in the way SRA formats/strips the data that we uploaded. However analysis can be fully replicated already using the information...
No it doesn’t just use the `run` command, `run10X` is just a convenience shortcut
I am not sure I understand what you mean. This is what you will get from the velocyto output: a loom file with spliced an unspliced . Or am I...
Yes then I understood well and gave you the answer in my previous message. The matrix IS the output of velocyto, it is stored in the loom file that you...
I solved compiler problem on Mac relying on compilers installed using conda (try both conda install gcc and llvm). I realize this solution is a bit vague, but I don't...
My favourite option is to install the conda version of gcc that will compile openMP without problems (see this answer https://github.com/velocyto-team/velocyto.py/issues/53 , It basically narrows down to this command: ``conda...
It is simply because your loom file does not contain such information, it is not supposed to, the notebook was of a particular example where we had precomputed those. In...
Exactly you can either: Write on the loom file using loompy Modify the vlm.ca in memory as you are suggesting Or just pass the variable to the downstream functions (for...
This is very weird, I tried to understand the problem but I don't have enough information. Do you think you could give me some extra info. For example what is...