Gioele La Manno

If you only need "any" loom file, surely you can change the format of your expression but if you need the special loom file that is used by velocity that...

This doesn't look like a problem in velocyto but rather a problem of its dependencies pysam/samtools. It could also be that the file is corrupted or something like that. Does...

Good to hear that it worked, sorry if I didn't point out that the problem could be a previously corrupted sorted bam file. You can pass any vector of labels...

Yes, beyond the line we discussed also the fact that the parameters are somehow assuming a dataset of the same size of the dentate gyrus one

This must be a problem related with the fact that you installed velocyto in an environment that has python 2.7 as default python, so that the pip3 installed programs are...

Igor is right, samtools is a requirement. Internally velocyto uses Popen to call samtools sort. I will change the instructions in the tutorial.

Sorry for the late reply, I think this is related to a different folder organization of a later/eralier version of cell ranger. I recommend using the `run` command and explicitly...

What is the command you are running?

I think you have the -e option in the wrong place, introducing the bamfiles. Try without. Sent from my mobile - excuse the typos

@naborasoledad this is not really the way one does issue reporting... I cannot help that much from the 4 copy-pasted lines of a traceback that you gave me there, sorry.