vireo

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Hi! Thank you for creating this tool, it has been very helpful. I have a pretty basic question regarding the output: in the file GT_barcodes.tsv, does the "cell" column contain...

Sharm8

Most cells are unassigned and a few of them do not match the filters

7

Hi, first of all, thank you for this tool. It has really saved our ass in a different experiment where HTO-based demultiplexing failed. Thank you a lot. I am running...

txemaheredia

A large number of cells are unassigned & very few n_vars

3

Hi, I ran vireo model 2 with my 10X multiome data (joint ATAC+RNA, a pool of 23 samples). But got a large number of unassigned cells, and very few n_vars...

nansne

Demultiplexing multiomic sequencing data

2

Hi @huangyh09, First of all, huge thanks for developing Vireo! I've been testing it using a synthetic pool (3 donors), and I've noticed a high number of unassigned cells, particularly...

DHelix

Hi! I'm interesting in reproducing your ELBO plot to determine the number of donors I have in a pool when demultiplexing without known donor genotypes, but instead thousand genomes reference....

jamesnemesh

Discriminative variants with GTbarcode

4

Dear all, Many thanks for the great tool and help on GitHub. I run Vireo and the results looks very promising (single cell RNAseq | mode 1a with genome 1k)....

flde

Beneficial to pool .bam files from seperate 10x single-cell lanes instead of demultilplexing seperately?

7

Hi - thanks for a nice tool! I have a quick question regarding the best approach for using cellsnp/vireo in our experimental setup: We have generated data from 8 separate...

koefoeden

Cells unassigned by using snp array

4

Hi, I was trying to demultiplex 20k cells to 4 donors. But only a few cells were assigned to each donor. each donor was genotyped using Infinium Omni2.5Exome-8 v1.5. The...

yilevine

I have scRNA-seq data where I have sequenced each individual separately and then all pooled together. I'm interested in turning these standalone samples into a genetic reference, but I'm not...

Ngort

Error when running vireo mode 2 with option -N 1

1

Hello vireo developers, I have a small issue to report, please see the details below: **Background** We're performing pooled single nucleus RNA-seq experiments, and are planning to demultiplex the samples...

calebthomas259