velocyto.py

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velocyto on non-UMI bam -U flag

2

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...

anafilia

AttributeError: 'NoneType' object has no attribute 'group', (gif file about Macaca)

1

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...

ogujessica

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...

rimmoussa

CellID in ca does not match the imported TSNE and cluster from cellranger files

1

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...

therealgenna

Deal with BD Rhapsody out file

4

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...

x1han

'VelocytoLoom' object has no attribute 'colorandum'

4

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...

spietrzak

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...

apredeus

Get tons of warnings when running

1

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...

dingyaozhang

WARNING - The .bam file refers to a chromosome not present in the annotation (.gtf) file

4

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...

sekekeretsu

Issues running velocyto

1

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...

Battamama