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velocyto-team / velocyto.py

RNA velocity estimation in Python
http://velocyto.org/velocyto.py/
BSD 2-Clause "Simplified" License
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Empty .loom file? #164

Open idalarsson opened 5 years ago

idalarsson commented 5 years ago

Hello, I'm trying to run velocyto on a 10x sample, and are running into a couple of issues. Some of them I think was resolved proberly but I'm still stuck on a couple of things.

(1) I get the same samtools error as in #163. After trying a number of things I realized that (since I used cellranger to process the raw data) the .bam-file is already proberly sorted as you mention in the CLI Usage Guide. I then tried to rename it cellsorted_genome_bam.bam instead of possorted_genomebam.bam, since you write that if a cellsorted[].bam file is already in the directory, the sorting process will be skipped.

This however doesn't seem to be the case? I can see that a sorting process starts when velocyto is run since temporary samtools-files are being created.

(2) When the run finishes, a .loom-file is created in the output-folder. But, this is only 27.3 MB large and when I import it into python and start the analysis, it seems like this is empty. Have you experienced this problem before and know what the error might be?

Best, Ida

mbrochut commented 6 months ago

Hello @idalarsson, I have the same problem as you, do you manage to solve it?