velocyto.py
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RNA velocity estimation in Python
I am trying to run velocyto run on a non-UMI bam file aligned using STAR. I am using -U flag, however velocyto still tries to find cell and UMI codes...
Hi, Velocyto team! I love velocyto, so I often use it with my mouse scRNAseq data etc. This time, I need to analyze scRNAseq data about Macaca. My collaborators ran...
Hello, I am running velocyto on a ~ 15 GB BAM file using the following command: `velocyto run10x /path/G1_blood/ /path/custom_gencode.vM29.annotation.gtf` but it's crashing due to a memory issue and giving...
Hi guys, I've run velocyto run10x (v. 0.17.17) to create loom file and when I loaded it into python and checked vlm.ca I saw that CellID disagrees with values imported...
Hi Velocyto team, Velocyto is an incredible tool to analysis RNA velocity information , and I have done many times on my 10X data, but I am getting some trouble...
I have recently generated a loom file using velocyto and I am currently trying to implement the analysis pipeline on it. However, I see the following error when I try...
Dear velocyto team, I was wondering what exact command is used to identify the reads overlapping the repeats, when this option is used? There are few ways of doing it...
When I tried to run your software, I got tons of warnings, but I do not know why it happens: `2023-10-22 22:23:04,235 - DEBUG - Counting for batch 24536, containing...
Dear Velocyto-experts, I am trying to perform RNA velocity analysis of 10x single cell data (cite seq) and during my velocyto executions I noticed warnings that the chromosome IDs in...
Hello, I am trying to make a loom file with velocyto.py. Every time I use this command: `velocyto run10x path_to_sample_folder mm10_rmsk.gtf ` I get this error: ``` OSError: truncated file...