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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. …
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Spatial single-cell quantification with alevin-fry
In this tutorial we will look at how to process a spatial gene expression (Visium) experiment using an alevin-fry based pipeline. Note : This tutorial is meant to mimic the original tutorial for spatial expression analysis with alevin written by Avi Srivastava. Thus, most of the descriptive text and commands are taken directly from that tutorial. However, here we will be analyzing the data using the alevin-fry pipeline instead of alevin. …
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Processing feature barcoding data with alevin-fry
In this tutorial we will look at how to process a CITE-seq experiment (a type of feature barcoding experiment) using an alevin-fry based pipeline. Note : This tutorial is meant to mimic the original tutorial for feature barcode analysis with alevin written by Avi Srivastava and Yuhan Hao. Thus, most of the descriptive text and commands are taken directly from that tutorial. However, here we will be analyzing the data using the alevin-fry pipeline instead of alevin. …
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An introduction to RNA-velocity using alevin-fry
Recently, RNA-velocity estimation has becomes increasingly popular tool in single-cell RNA seq analysis. In this post, we will discuss an additional advantage brought by the Unspliced-Spliced-Ambiguous (USA) mode introduced in alevin-fry 0.3.0 and later. That is, the solution presented in that approach for controlling the spurious mapping to spliced transcripts of sequenced fragments arising from introns (in the absence of full decoy) basically gives us the preprocessing results we need to perform an RNA-velocity analysis “for free”. Here we provide an end-to-end tutorial describing how to perform an RNA-velocity analysis for a 10x Chromium dataset. In this tutorial, we will show the whole analysis pipeline, starting from the raw FASTQ files to the gorgeous velocity plots (generated by scVelo) that you may like to include in your next analysis or paper. …