Empty .loom file?

[idalarsson]

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_genome_bam.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]

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