How to load count matrix of scRNAseq data from cel-seq2 (96 well plates) protocol into a Seurat object
I have count matrix scRNAseq data from cel-seq2 (96 well plates) protocol for few samples which are tab separated text files in which the rows are genes and the columns are cells from different wells in the plate.
I have no experience of working with cel-seq2 which is different from 10X genomics. I found a tool with the same name from here:
https://github.com/yanailab/celseq2
but so far I did not manage to get it working. since I already have count matrix, is it possible to use Seurat R package for this data? if so, how can I load this data to a Seurat object
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Extracting normalized counts from RDS (Seurat) file
written by uyeiveycdikcdukyoz •
-
Large-scale bulk RNAseq Experiment with abnormal MA-plots for apoptotic conditions
written by Nico •
-
Most appropriate method to analysing multi-plate single concentration drug screening
written by yura.grabovska •
-
scRNA-seq: To merge technical sequencing replicates or not to merge?
written by Kanai •
-
cellranger count output does not give all genes.
written by Adem80 •
-
Differential Expression Analysis in Single cell RNAseq
written by asumani
-
Batch effect correction
written by goldie.ed •
-
Randomizing 384 Samples Among 4 96-Well Plates With Covariates
written by David Quigley
-
Detecting Trace Contamiants In Sanger Sequencing
written by Swbarnes2
-
Programming The Beckman Coulter Biomek Fx Robot
written by Weronika
You can use
CreateSeuratObject: https://www.rdocumentation.org/packages/Seurat/versions/3.0.1/topics/CreateSeuratObject