Tag: Alevin

Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cell Ranger.

Looks like 10x has example datasets on their web site. Will take a look to see what these BC sequences look in reality. Should be possible to bin them using seal.sh from BBMap. Edit: From one of the test datasets it is possible to see these BC barcodes in Read…

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Bulk RNAseq Salmon index building which transcriptome to use

Bulk RNAseq Salmon index building which transcriptome to use 0 Hi all, I am new to the platform. I was wondering what the common/best practice is regarding building a Salmon index for bulk RNAseq analysis of human cells. The tutorial for Salmon/Alevin is using the complete transcriptome from GENCODE (gencode.vM23.transcripts.fa.gz,…

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Create seurat inputs without cellranger

Create seurat inputs without cellranger 1 “Hey there! I’m really curious about creating Seurat inputs without using Cell Ranger, as we’ve got our own sequencer and have done the sequencing in-house. Has anyone else tried this approach or can offer some guidance on how to go about it? Any help…

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Single Cell Pipeline for SmartSeq

Single Cell Pipeline for SmartSeq 1 Dear Community, I want to align SmartSeq platform-based single-cell data to the human genome using Alevin and/or StarSolo and then create a Seurat object. My data is paired-end. Each FASTQ file is around 4-10 GB in size. R1 and R2 pairs look like this:…

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scrnaseq: Introduction

Introduction nf-core/scrnaseq is a bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data. This is a community effort in building a pipeline capable to support: Alevin-Fry + AlevinQC STARSolo Kallisto + BUStools Cellranger UniverSC Documentation The nf-core/scrnaseq pipeline comes with documentation about the pipeline usage, parameters and output….

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Adding Salmon Alevin counts to clustered Seurat object

Adding Salmon Alevin counts to clustered Seurat object 0 Hi Im trying to figure out an appropriate way to add Salmon Alevin count matrix to a previously created and clustered Seurat object, just to be able to see isoform distribution across clusters generated from scRNA-seq data. I can import Alevin…

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Is it possible to use salmon alevin tool for total rna seq samples?

Is it possible to use salmon alevin tool for total rna seq samples? 1 Hi All, I’m interested to quantify the propositions of spliced vs unspliced transcripts at transcript level. As pointed out this page(combine-lab.github.io/alevin-tutorial/2020/alevin-velocity/). But they used single-RNA sequencing data so, it is salmon alevin. But what i did…

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Bioconductor – tximport

DOI: 10.18129/B9.bioc.tximport     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see tximport. Import and summarize transcript-level estimates for transcript- and gene-level analysis Bioconductor version: 3.13 Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level…

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Applications of single-cell RNA sequencing in drug discovery and development

DiMasi, J. A., Grabowski, H. G. & Hansen, R. W. Innovation in the pharmaceutical industry: new estimates of R&D costs. J. Health Econ. 47, 20–33 (2016). Article  PubMed  Google Scholar  Wouters, O. J., McKee, M. & Luyten, J. Estimated research and development investment needed to bring a new medicine to…

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The Biostar Herald for Monday, April 03, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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Transcriptional reprogramming of skeletal muscle stem cells by the niche environment

Isolation of pure populations of MuSCs and niche cells by fluorescence-activated cell sorting (FACS) Hindlimb muscles were dissected from young (4–6 weeks old) or aged (22–26 months old) C57BL/6J (Jackson Laboratory, 000664) mice and minced until no visible tissue chunks were visible. Muscle was then digested in a 15 ml Falcon…

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SALMON Index build Process Killed!

SALMON Index build Process Killed! 0 Hello, I was trying to create an decoy-aware index with Salmon (v1.4.0). So I used primary-assembly genome file and transcript file from Gencode library and followed the steps mentioned in the combine-lab.github.io/alevin-tutorial/2019/selective-alignment. Concatenated transcript file with genome to create gentrome.fa.gz. Then tried to create…

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Tools/pipeline for analysis of smart-seq3 data

Tools/pipeline for analysis of smart-seq3 data 1 I have Smart-Seq3 data and zUMIs refuses to work. Is there any other alternative? Nf-core pipelines rnaseq and scrnaseq doesn’t support sm3 yet. I am also prepared to go down the manual route. Has anyone tried umi_tools or alevin at least to demultiplex…

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Alternatives and detailed information of monocle3

Licence: other No description or website provided. Projects that are alternatives of or similar to monocle3 dropEst Pipeline for initial analysis of droplet-based single-cell RNA-seq data Stars: ✭ 71 (-58.24%) Mutual labels:  single-cell-rna-seq StackedDAE Stacked Denoising AutoEncoder based on TensorFlow Stars: ✭ 23 (-86.47%) Mutual labels:  single-cell-rna-seq kmer-homology-paper Manuscript for functional prediction…

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New Single-Cell ‘Total’ RNA-seq Method Promises More Comprehensive Transcriptome View

This story has been updated to correct information about methods developed by Hao Wu.  NEW YORK – A new method for single-cell RNA sequencing may provide a triple threat: high sensitivity, full-length coverage of RNA, and high throughput. The researchers behind the method — dubbed “vast transcriptome analysis of single cells…

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Quick questions about Alevin and AlevinQC

I have just started using Alevin and I have few basic queries. And I am asking this because I couldn’t find it in the documentation How to know how many reads are uniquely mapping and how many are multi mapping when doing quantification with Alevin. The alevin_meta_info.json says Number of…

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