The Cell Ranger v3.0.1 software suite was obtained from 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest). Raw sequencing data were first de-multiplexed and quality checked using the ‘mkfastq’ script. For all libraries, alignment and transcript...
Raw scRNA-seq data were processed using the Cell Ranger Single-Cell Software Suite20 (v3.0.0, 10x Genomics). In brief, reads were first assigned to cells and then aligned to the human genome using STAR51, with the hg38 build of the human genome (GRCh38) as a reference for alignment....
The raw single-cell RNA-seq dataset was performed demultiplexing, barcode assignment, and UMI quantification with aligned to reference-grade TM-1 genome [78] (http://cotton.hzau.edu.cn/EN/Download.htm) using the Cell Ranger Software Suite (v4.0.0). A total of 91.3% mapping rate and more...
The Cell Ranger Single-Cell Software Suite v3.01 was used to perform sample demultiplexing, barcode processing, and quality control filtering and integrating. The integrated dataset has 55,241 cells in the gene-cell-barcode matrix that includes a total 25,885 and 29,356 cells from the 3 ...
The command Cell Ranger count in CellRanger Software Suite (10x Genomics) was used to demultiplex and barcode the sequences derived from the 10x Genomics single-cell RNA-seq platform. The data was filtered, normalized, dimensionality was reduced, clustered, and differential gene expression analysis ...
10x Genomics Cell Ranger 5.0.0 Zheng et al., 2017 https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome Seurat v.4.0.3 Stuart et al., 2019 https://satijalab.org/seurat/ SCTransform Hafemeister and Satija, 2019 https://github.com/ChristophH/sctransform Harmony...
The 10x Genomics Cell Ranger 5.0.1 software suite69 was used to perform sample de-multiplexing, barcode processing, and single-cell 3’ gene counting. The cDNA insert was aligned to the hg38/GRCh38 reference genome. Only confidently mapped, non-PCR duplicates with valid barcodes and unique ...
The Cell Ranger Single Cell Software Suite version 2.1.0 (10X Genomics, Inc.) was used for alignment, de-multiplexing, and UMI counting using the default parameters. Sequencing metrics are presented in Table S1. From 15 samples, 45,547 single cells were collected, ranging from 1413 to 7983...
It is same to the "matrix.mtx" file in the CellRanger output of a 10X dataset. The order of cells should be the same with "filtered_cells.csv". The order of peaks should be the same with "top_filtered_peaks.bed. 3. Functions of APEC (step by step) Users can directly run ...
The Cell Ranger Software Suite (v6.1.1) was used to perform sample de-multiplexing, barcode processing and single-cell 3′ unique molecular identifier (UMI) counting with the mm10 reference mouse genome obtained from Ensembl. Specifically, Spliced Transcripts Alignment to a Reference (STAR) was ...