velocyto.py
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velocyto-team
RNA velocity estimation in Python
Hi there, I'm getting a different error that I haven't seen reported in the other installation problem issues. I'm using python 3.6.1, have tkinter installed, and have a fresh conda...
Hello: When I run `velocyto run10x`: ``` velocyto run10x -@ 64 -m /lila/data/chen/dan/ref/gtf/mm10_rmsk.gtf \ TCD_1 \ /lila/data/chen/dan/ref/gtf/Mus_musculus.GRCm38.93.gtf ``` I found this error: ``` Traceback (most recent call last): File "/home/lid/miniconda3/bin/velocyto",...
Commands to reproduce: ```` conda create -n velocyto python=3.9 conda activate velocyto conda install numpy scipy cython numba matplotlib scikit-learn h5py click pip install velocyto velocyto --help ```` Output ````...
Hi, I would greatly appreciate any insights into the following issues. The biggest yellow flag is that the .loom file generated from a recent 10X Chromium dataset (using the separate...
Hello I use velocyto to count spliced / unspliced counts on dropseq data I use the command `velocyto run -o ./loom/ -m /cluster/huanglab/hhuang/Database/RNA_velocity/rmsk/hg19/hg19_rmsk.gtf /cluster/huanglab/hhuang/project/jing/Work/2020.7.22/data_ziwei_new_alignment/CH4-LN_S1_L001_b37/star_gene_exon_tagged.bam /cluster/huanglab/hhuang/project/jing/Final_ziwei_data/20200701/Homo_sapiens.GRCh37.75.gtf` **without -b parameter** But when...
Hello, this is a amazing tool. I have some problems when I analysis Dropseq data. Maybe you have some expriences can help me solve these problems 1. After the pipeline...
Hi velocyto-team, Velocyto.py is a powerful pipline for single cell RNAseq analysis, thanks a lot to your excellent job. I'm fresh in RNA velocity ananlysis and recently I met some...
Hey, I am having memory problems in velocyto run: [elenasl@cicdna ~]$ velocyto run --bcfile /home/elenasl/scRNAseq/cellranger/run_msc_CTL_Ranger_count/outs/filtered_feature_bc_matrix/barcodes.tsv.gz --outputfolder /home/elenasl/scRNAseq/scvelo --samtools-threads 16 --samtools-memory 120000 /home/elenasl/scRNAseq/cellranger/run_msc_CTL_Ranger_count/outs/possorted_genome_bam.bam /home/elenasl/scRNAseq/cellranger/refdata/refdata-gex-GRCh38-2020-A/genes/genes.gtf 2> velocyto_control.err > velocyto_CTL.outs [elenasl@cicdna ~]$ cat...
Attempting to install velocyto on mac OS monterey 12.4, and running into a similar error I have seen on other issue threads. When running `pip install velocyto` after [installing dependencies...
Hello velocyto maintainers, I am working with a dataset where the barcodes (CB) and UMIs (UR) are not in the standard string sequence format. Specifically, my barcodes are represented as...
