velocyto.py

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possorted_genome_bam.bam file not found in cellranger output folder

1

I am trying to run velocyto to generate loom files needed for scvelo analysis. It appears that I lack a the "possorted_genome_bam.bam" file needed for velocyto in the cellranger output...

tangybat

how velocyto fits to cellrange-arc output

2

hi, how velocyto fits to cellrange-arc output, velocyto is designed for cellrange cout output with the bam file named "possorted_genome_bam.bam", but cellrange-arc output with the bam file named "gex_possorted_bam.bam". how...

zqmiao-mzq

Hi, I ran into a bug at the last step. It seems it is caused by the loompy. But I followed the install instructions to install every package and the...

zcaiwei

I am running velocyto on slurm. I tried to pass samtools memory spec via `--samtools-memory 64G` and `--samtools-memory $((8*8042))` Both times I received an error. `Error: Invalid value for '--samtools-memory':...

wudustan

Batch effects in combining multiple loom files

2

I have samples are the spread across batches and I'm running velocyto for each batch (having its own cellranger folder) separately and finally combining all the loom files into one....

anshu957

running run-dropest

4

Hi, I am having trouble trying to follow the tutorial (http://velocyto.org/velocyto.py/tutorial/cli.html#run-dropest-run-on-dropseq-indrops-and-other-techniques). The data I was working with were prepared using celseq2 with bp1-bp6 as UMI and bp7-bp12 as cell barcodes....

bxxu

ERRORS when running velocyto: ERROR - This is an older version of cellranger, cannot check if the output are ready, make sure of this yourself! ERROR - Can not locate the barcodes.tsv file!

2

Good afternoon Velocyto team, I know many users run into this issue, but I could not fix it by what was offered in the community. I am running velocyto in...

AsyaTiho

Hi there, When running `velocity run10X` (#373), I encountered the error below. Would you mind giving me some advice to address it? `velocyto run10x -m /ceph/project/......../mm10_rmsk_chrMTGTF.gtf /ceph/project/........./10x_scRNA_704-187_CD8P_GEX /ceph/project/......./genes/genes.gtf` Thank you....

denvercal1234GitHub

run command fails due to write permissions

4

Hi there! This should be an easy fix, but just wanted to report that velocyto run fails in the event that the user running it does not have write permissions...

gabprg

Error in run10X: logging.debug(f"Example of barcode: {valid_bcs_list[0].split('-')[0]} and cell_id: {valid_cellid_list[0]}") - IndexError: list index out of range

1

Hi there, I was running `velocyto run10x -m /ceph/project/....../mm10_rmsk_chrMTGTF.gtf /ceph/project/........../10x_scRNA_704-187_CD8P_GEX /ceph/project/borrowlab/shared/scRNASeq_blood_220210/xenon/Blood_CD8T_TranscriptomeTCRseq/Blood_CD8T_scTranscriptome/run_cellranger_count_chrMTGTF/refdata-gex-GRCh38-2020-A_chrMTGTF/genes/genes.gtf` The `/ceph/project/........../10x_scRNA_704-187_CD8P_GEX` points to the folder `10x_scRNA_704-187_CD8P_GEX` that contains my `outs` folder, which contains the `possorted_genome_bam.bam` that I had...

denvercal1234GitHub