vireo

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assignments between snRNA and snATAC

3

We have snRNA & snATAC from pooled samples on which we ran vireo; is there a way to determine how consistent the assignments are btw RNA and ATAC? Thanks you!

Parul-Kudtarkar

Strategies for validating output

4

Hello, Thank you for creating this useful package (and also the genotyping package, cellsnp-lite) that has been critical to my work in bone marrow transplant research. I have ran the...

hongdavid94

Memory overload for large number of patients

3

I am trying to demultiplex 8000 cells that pooled 63 patients together using the following: ``` vireo -t GT -N 63 \ --vartrixData=${VARDIR}/vt_alt.mtx,${VARDIR}/vt_ref.mtx,${BC},${VCF} \ -d ${VCF} -o $OUTDIR ``` but...

racng

Vireo without Genotype (N=3) - high unassigned cells

2

Hi @huangyh09, Thank you for creating vireo & cellsnp-lite - it is my to go software for demultiplexing!! We have multiomic sequencing (shallow) 1. for scRNA 3320 mean raw reads...

Parul-Kudtarkar

Hi, First of all, thank you so much for developing cellsnp-lite and vireo, it has saved our lab a lot of money. I'm used to run them on scRNA-seq data...

DanielMedinaCano

All cells unassigned in 10x snRNA-seq data

3

Hello, Thank you so much for creating Vireo, it’s been very useful for us! I am currently using cellsnp-lite and vireo to demultiplex my single cell snRNA-seq data (pool of...

ninasachdev

Proper steps for cellSNP and Vireo for large dataset

4

Hi. I have been working on a set of data with 20K cells, and I have few questions regarding how to approach the data. Q1: For cellSNP, it was taking...

vincycheng

Subsetting a vcf file

1

Dear vireo developers, Thank you very much for your really nice package. I have a question regarding finding the discriminatory variants between groups of donors that vireo found. The overall...

WWolf

vireo and large dataset

1

Hi, I am trying to use vireo with large data (the cellSNP.cells.vcf is 7GB) and it stoppes running after 5 secondes of loading cell VCF file. command line : vireo...

HibaLaghrissi

Which VCF files to use for SNP calling?

1

Hi, thanks for developing this tool for genotyping. I performed SNP calling with cellsnp-lite, with either (7.4M SNPs with minor allele frequency (MAF) > 0.05) or (36.6M SNPs with minor...

ShouWenWang