velocyto.py
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velocyto-team
RNA velocity estimation in Python
Error:: below error is occured when running velocyto with cellranger-5.0.1-dirty. with cellranger 7.0.0 version is OK. OSError: truncated file [E::bgzf_uncompress] CRC32 checksum mismatch [E::bgzf_read_block] BGZF decode jobs returned error 1...
I'm trying to run Velocyto on a Linux. I can't seem to get around this error. I've also tried to sort manually with no luck. I've been trying to sort...
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...
Hi there, Thanks for the package. I obtained a very high % of unspliced reads (65%) in the samples of human tonsils. Do you know if this high % is...
The code does not stop, but it gave a "could not retrieve index file for cellsorted_possorted_genome_bam.bam" I did not do the sorting before running velocyto. Should I be worried? 2024-01-13...
I want to use ENSEMBL annotations because my CellRanger output was aligned using GRCh38 v 32 (Ensembl 98). For that matter, I have the fasta sequence of the corresponding release,...
Hi there, Thank you for the package. Would anyone clarify when should we consider using the `repeat annotation mask`? And, whether it is a "soft" or "hard" masking? In most...
Hi team！I've recently encounted some questions about the method in the article. In the velocity analysis, we only have the unspliced count and spliced count according to the velocyto program,...
When running velocyto on 10x data in default format, I get the error message stated in the title. Full error log (velocyto) velocyto % sh run_velocyto_1.sh OMP: Info #276: omp_set_nested...
Hi. when I run "velocyto --help",I got the errors. How to fix it? Thank you. $ velocyto --help Traceback (most recent call last): File "/home/lxl/softwares/miniconda/miniconda3/envs/velocytoP38/bin/velocyto", line 5, in from velocyto.commands.velocyto...
