velocyto.py
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velocyto-team
RNA velocity estimation in Python
Hi, I follow the instruction in the tutorial in order to produce the loom file for scVelo. but when I run the velocyto tools dropest-bc-correct, it reports tag "CB" is...
Hi, I am trying to run velocyto using run10x command. I'm running on cluster by requesting 60 GB memory. Do I need more memory for that? Thank you so much...
Hello, When I run run10x command on the 10X samples aggregated using cellranger aggr function, run10x gives me an error. Traceback (most recent call last): File "../anaconda3/bin/velocyto", line 11, in...
Hi this is a similar to issue to some of the GTF error issues other people have raised but I saw the solution was removing a field from the annotation...
Can someone please post the sample .bam file for the velocyto python notebooks for which i can myself generate the loom file.
Hi, I have installed and running velocyto on my Mac with 16GB RAM. The data I am processing is 10X data single cell. Using CLI, velocyto stuck for several hours:...
Hi, I realized that some of the genes that are not shared for both spliced and unspliced info are filtered in the beginning of the velocyto pipeline. During the velocity...
Hi i'm using the human week 10 fetal forebrain dataset(SRP129388) in your paper to do the velocyto. I hava downloaded SRR6470906.sra and SRR6470907.sra and use fastq-dump --split-3 --gzip to get...
Hi All， I am running velocyto.py to process the 10x PBMCs data (v3.0.0). My code is 'velocyto run10x -m cellranger-3.0.0/reference/expressed_repeats_annotation/hg38_rmsk.gtf cellranger-3.0.0/sample01 cellranger-3.0.0/reference/refdata-cellranger-GRCh38-3.0.0/genes/genes.gtf' And it returns 'Error: Invalid value for 'GTFFILE':...
If I analyze Single-nuclei RNA-seq (snRNA-seq) data, which parameter should I use? I don't know `run10x` and `run_dropest` which one I should use. Or velocyto can't analysis snRNA-seq data? Thanks...
