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linnarsson-lab / loompy

Python implementation of the Loom file format - http://loompy.org
BSD 2-Clause "Simplified" License
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Running Velocyto Command Error #146

Open josinejansen opened 3 years ago

josinejansen commented 3 years ago

Dear Linnarsson lab,

I am quite new to programming, and only started working with single cell data in April 2020. I have a question and was hoping you would be willing to respond and help me pave my way to run RNA velocity on my samples.

My problem is that when I am trying to follow the Velocyto instructions ('getting started', 'preparation', and 'running Velocyto' on 10x samples) I get stuck:

I downloaded a human reference genome sequence for the 10x website set (.gtf) and a human expressed repeat annotation file (.gtf) from the USCS genome browser, and uploaded them in my JupiterLab Folder. But when I run the following command velocyto run10x -m repeat_msk.gtf mypath/sample01 somepath/refdata-cellranger-mm10-1.2.0/genes/genes.gtf

(in my case it looks like this: velocyto run10x -m('MASK_expressed_repeats_annotation.gtf') 'filtered_feature_bc_matrix.h5'/refdata-cellranger-mm10-1.2.0/genes/'genes.gtf)

I get an error:

image

When I read the information on the input files ("Requirements on the input files" : http://velocyto.org/velocyto.py/tutorial/cli.html) it is mentioned that it needs a bam file, which wasn't mentioned under run10x, where it says the command needs a filtered_bc_matrix file. Anyway, when I try it with the possorted_genome_bam.bam output file from Cell Ranger the system throws the same error unfortunately.

My eventual goal is to run RNA velocity on specific cells from 2 organs (3 patients in total) to check if we can obtain any information about their directionality. I have subsetted an Anndata object with around 600 cells based on their barcode.

Please let me know if I can reach out to you for further guidance :-) Thanks in advance for taking the time to read my message!

Josephina

denvercal1234GitHub commented 2 years ago

Check on https://github.com/velocyto-team/velocyto.py/issues. Some of your questions might have been answered there?