vireo

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Vireo taking ages to run

4

Hi, I have some single-cell RNA-seq data for which I don't have genotype information. I ran cellSNP-lite on a merged BAM file containing all of the donors to genotype the...

lucygarner

Question: Bulk RNA-seq from nanopore?

1

Hi! Impressive work! I was wondering whether your package would support demultiplexing bulk RNA-seq? And nanopore-based (i.e. not Illumina short) reads? Is support for other genomes (e.g. other mammalians) easily...

alexandruioanvoda

all unassigned for 10x single cell RNAseq dataset using 1000genome vcf

3

Hi Huang, Thanks for reading my previous issue. I had another problem. I am trying to apply vireo with scRNAseq datasets based on 1000 genome vcf file. However, all the...

songeric1107

Clarifying the workflow using bulk RNA-seq data for genotyping

1

Hi, I have bulk RNA-seq data for each of my human samples, plus the scRNA-seq data that I would like to demultiplex with Vireo. Could I just clarify the workflow?...

lucygarner

combine multiple donor vcf

8

Hello, I have 2 pooled snATAC donors and their individual bulk RNA-seq data. To demultiplex, my strategy was to call common variant SNPs for the two individuals separately using CellSNP,...

AnjaliC4

Does running Vireo in linux without a genotype file require the sparse matrix to be in vcf format?

1

I am attempting to run vireo to demultiplex my single-cell RNA-Seq data (2 donors). I do not have genotype data. I have converted my counts data to a sparse matrix,...

alexisweber

Large number of `doublet` and `unassigned`, most lost from specific donor(s), after removing doublets

6

Hi, I'm running `cellsnp-lite` (`v1.2.0`) and `vireo` (~`v0.5.5`~ `v0.5.0` from pip) to demultiplex a 3' 10X scRNA-seq dataset with cells from 8 human donors. These cells were pooled and run...

PeteHaitch

high unassigned in 10x single nucleus RNA seq

1

Hi Huang, Thanks for reading my issue. I am trying to apply cellSNP and vireo on 10x single nucleus RNA seq. However, the unassigned nuclei are quite high. Var1 |...

evolanna

ImportError..... failed to map segment from shared object: Cannot allocate memory

1

Hi, I installed vireo and tested successfully with the examples in the package. While running with my own data, the job error out after an hour: `Traceback (most recent call...

maojn

Different result with same file and cmd

2

Hi, Thanks for great tool for donor ananylsis. I got different results with same file and cmd, I do not know why?  Best

mengchengyao