Tag: MARS-seq

nf-core/marsseq

Introduction nf-core/marsseq is a bioinformatics single-cell preprocessing pipeline for MARS-seq v2.0 experiments. MARS-seq is a plate-based technique that can be combined with FACS in order to study rare populations of cells. On top of the pre-existing pipeline, we have developed an RNA velocity workflow that can be used to study…

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nf-core/marsseq: systematic pre-processing pipeline for MARS-seq experiments

Abstract As a result of advancing single sequencing technology (scRNA-seq), it has become possible to study gene regulatory mechanism(s) and their influence on evolving cell states in time at the level of individual cells. Since 2009, numerous scRNA-seq protocols have been developed, each with its own advantages, disadvantages and library…

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systematic pre-processing pipeline for MARS-seq experiments

%PDF-1.4 % 93 0 obj <> endobj 113 0 obj <>stream application/pdf Martin Proks nf-core/marsseq: systematic pre-processing pipeline for MARS-seq experiments 2023-06-08T07:43:26Z Word 2023-06-30T02:12:09-07:00 2023-06-30T02:12:09-07:00 macOS Version 13.4 (Build 22F66) Quartz PDFContext uuid:98ec5752-1dd1-11b2-0a00-8a0827bd7700 uuid:98ec575e-1dd1-11b2-0a00-900000000000 endstream endobj 5 0 obj <> endobj 2 0 obj <> endobj 90 0 obj <> endobj…

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How to analyze mars-seq single end-read scRNAseq data?

How to analyze mars-seq single end-read scRNAseq data? 1 I am new to cellranger and mapping. I want to analyze a SRR2319344 scRNA-seq data which only has single-end read. But cellranger count requires paired end reads (R1 R2). May I ask how to analyze this SRA data? Thanks cellranger single-end…

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Solved a. Explain (with drawings too, if you’d like!) how

Transcribed image text: a. Explain (with drawings too, if you’d like!) how droplet single-cell mRNA sequencing works at the molecular level. (3pts) b. Why is this so useful? What can this technology offer that we don’t get with bulk DNA sequencing, RNA sequencing, or simpler single-cell RNA sequencing methods (like…

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How to use MARS-seq dataset for 10X scRNA-seq cluster annotation (i.e. convert the dataset to Seurat object)

How to use MARS-seq dataset for 10X scRNA-seq cluster annotation (i.e. convert the dataset to Seurat object) 0 Hi, I am new to single-cell sequencing analysis. I performed 10x scRNA-seq and found the only suitable research paper on single-cell sequencing of the same tissue site. But their single-cell sequencing uses…

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