What aligner does Cellranger use?
STAR
Cell Ranger uses an aligner called STAR, which peforms splicing-aware alignment of reads to the genome.
What is feature barcoding 10X?
Feature Barcode technology is a method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays. Look for the Feature Barcode icon in the content menu at left for documentation specific to Feature Barcode Technology.
What is Scatac seq?
What is ATAC-Seq? The ATAC-Seq method is a genome-wide NGS-based assay that characterizes chromatin states in cell and tissue samples. In particular, ATAC-Seq is used to identify regions of the genome that have open chromatin states that are generally associated with sites undergoing active transcription.
What does 10X genomics do?
The 10X Genomics technology generates individually barcoded sequencing libraries for hundreds of thousands of nanoliter volume oil droplets using up to 1.7 million different barcodes. Thus, it allows individual long DNA molecules 10X Genomics Chromium Genome Linked-reads principle.
How does feature barcoding work?
“Feature Barcoding” refers to using antibodies linked to specific oligos. The antibodies can then bind to cell surface markers of interest and the oligos they’re conjugated with turned into normal scRNA-seq reads.
What are the pipelines in cell Ranger software?
Cell Ranger includes four pipelines relevant to the 3′ Single Cell Gene Expression Solution and related products: cellranger mkfastq demultiplexes raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
How to analyze scRNA-Seq data from Nature publication?
This guide outlines how to perform the analysis, and what results 10x assays and software produce using data from a recent Nature publication “Single-cell transcriptomes of the regenerating intestine reveal a revival stem cell” (2019; doi: 10.1038/s41586-019-1154-y).
What is cell Ranger in 10x Genomics support?
-Software -Single Cell Gene Expression -Official 10x Genomics Support What is Cell Ranger? Cell Ranger is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.
Which is sample format for cellranger mkfastq pipeline?
The cellranger mkfastq pipeline can also be run with a samplesheet in the Illumina Experiment Manager (IEM) format. If you didn’t sequence with sample indices, you’ll need to use this format. Briefly look at cellranger-tiny-bcl-samplesheet-1.2.0.csv before running the pipeline.
https://www.youtube.com/watch?v=9YXRoaQyixQ