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Processing 10x Flex Gene Expression data with simpleaf
Simpleaf is a command line toolkit written in rust that exposes a unified, simplified interface for processing single-cell and single-nucleus sequencing data using the alevin-fry pipeline. In this tutorial, you will learn how to use simpleaf multiplex-quant to process 10x Genomics Flex Gene Expression (Fixed RNA Profiling) data. …
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Generating a spatial transcriptomics count matrix with simpleaf
Simpleaf is a command line toolkit written in rust that exposes a unified, simplified interface for processing scRNA-seq datasets using the alevin-fry pipeline. …
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Operating on the Registry of Custom Chemistries in Simpleaf
Simpleaf is a command line toolkit written in rust that exposes a unified and simplified interface for processing scRNA-seq datasets using the alevin-fry pipeline. …
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Developing a custom simpleaf workflow from scratch
Simpleaf is a command-line toolkit written in Rust that exposes a unified and simplified interface for processing scRNA-seq datasets using the alevin-fry ecosystem of tools. Since Simpleaf version 0.15.0, we introduce the re-designed simpleaf workflow sub-program, which provides the ability to execute complex and highly-configurable single-cell data processing workflows consisting of Simpleaf commands and shell commands described by a simple user-provided Jsonnet program. One can fetch ready-made Simpleaf workflow templates from our protocol library, protocol estuary, using the simpleaf workflow get program, or develop custom workflows to achieve specific tasks. This tutorial will discuss how to build a valid Simpleaf workflow template from scratch. If you are interested in running an existing workflow, please check our tutorial about running Simpleaf workflows. …
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Executing single-cell data processing workflows with simpleaf
Simpleaf is a command line toolkit written in rust that exposes a unified and simplified interface for processing scRNA-seq datasets using the alevin-fry ecosystem of tools. In simpleaf version 0.15.0, we introduce the re-designed simpleaf workflow module, which provides the ability to execute complex and highly-configurable single-cell data processing workflows consisting of simpleaf commands and shell commands, described by simple user-provided Jsonnet programs. One can fetch published simpleaf workflow templates from our protocol library, protocol estuary, using the simpleaf workflow get program or develop custom templates to achieve specific tasks. …
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Generating a scRNA-seq count matrix with simpleaf
Simpleaf is a command line toolkit written in rust that exposes a unified and simplified interface for processing scRNA-seq datasets using the alevin-fry pipeline. It encapsulates the whole alevin-fry pipeline into two steps: simpleaf index indexes the provided reference or makes an expanded reference and indexes it. simpleaf quant maps the sequencing reads in provided FASTQ files against the indexed reference and quantifies the mapping records to generate a gene count matrix. …
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Analysing split-seq data using salmon and alevin-fry pipeline
Authors: Gaurav Sharma, Computational Biologist at Ocean Genomics; Jeremy Simon, Assistant Professor at UNC Chapel Hill; Rob Patro, Cofounder at Ocean Genomics This project has been made possible by the team at Ocean Genomics, and by a grant from the Chan Zuckerberg Initiative. …
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How to run many different sc-RNA-seq protocols using salmon alevin's custom geometry
Author: Gaurav Sharma, Computational Biologist at Ocean Genomics This project has been made possible by the team at Ocean Genomics, and by a grant from the Chan Zuckerberg Initiative. …
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Analysing sci-RNA-seq3 data using salmon and alevin-fry pipeline
Author: Gaurav Sharma, Computational Biologist at Ocean Genomics This project has been made possible by the team at Ocean Genomics, and by a grant from the Chan Zuckerberg Initiative. …
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A quick start guide to a portable and simplified alevin-fry pipeline
Here, we show how to perform a complete analysis on the 1k PBMCs from a Healthy Donor data from 10X Genomics. This run through includes all steps, even extracting the splici sequence and building the salmon index, which you typically would not do per-sample. To make this sample as easy as possible to follow, we have bundled all of the required software and utilities in a singularity container that we use in the commands below. …