biomart811

Alignment of assembly on reference genome with MiniMap2 returns false unmapped contig

3

Hi everybody, I have used MiniMap2 to map an assembled genome (generated with oxford nanopore reads) on a public reference, I did it to find the regions in common and...

cell state label is mandatory ?

2

Hi, I would like to use BayesPrism on rnaseq data, is it mandatory to have also a file which specify the cell state label of my single cell data? Or...

Z expression matrix

7

Hello, I would like to know what is the step in Bayes Prism where the Z matrix, that we found in posterior.initial.state/type, is generated? Thanks a lot for your help

Hello everyone, I am trying to use bulk2space but I get the following error message. I think there is something wrong when my bulk and my sc-panel interact because if...

Pysamstats: supplementary alignments

1

Hi everybody. I have used pysamstat to calculate some statistics on my bam file. I saw on IGV that in the region of interest of bam file, where I used...

using scMerge2 with count matrix Seurat object

1

Hello everyone! I would like to integrate 2 datasets of single cell using scMerge2. I have the two rds objects, coming from Seurat, containing the counts matrices for each dataset...

Error with bsbolt index

1

Hi everyone, I get an error when try to index with bsbolt Index:I try to index the ref genome of hg38 only with -G and -DB but it shows index:...

Format of batch input : vector or factor ?

1

Hello, I noticed an issue while using kBET with the subsampling of my data, basically I saw differences in the result ok kBET if I declare batch as vector rather...

kBET on Harmony or CCA integration

1

Hello! I am trying to use kBET on a very large integrated dataset (40.000 genes across 180.000 cells). I have few question about it. 1) Since both Harmony and CCA...

Clarification on high rejection rates with large single-cell dataset (~200k cells)

1

Hi, I’m working on a large single-cell RNA-seq dataset consisting of approximately 200,000 cells and four distinct batches. I’ve been using kBET to evaluate batch correction after integration, but I...