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author gaelcge
date Tue, 02 Aug 2022 19:40:03 +0000
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            ***** links to input data for 10X single-analysis and Seurat tutorials ****
                                               ****

***** Single-Cell ATACseq (10X Genomics) - from fastq to dimentionality reduction

Fastq = https://support.10xgenomics.com/single-cell-atac/datasets/1.2.0/atac_v1_pbmc_5k
small_fastq_files = https://support.10xgenomics.com/single-cell-atac/datasets/2.0.0/atac_pbmc_500_nextgem

Software = Cell Ranger ATAC 1.2.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/installation)

Tutorial from cell ranger output to clustering = https://satijalab.org/signac/articles/pbmc_vignette.html



****** Multiome (ARC) = scRNA + scATACseq (10X Genomics) - from fastq to dimentionality reduction

Fastq = https://support.10xgenomics.com/single-cell-multiome-atac-gex/datasets/1.0.0/pbmc_unsorted_3k

Software = Cell Ranger ARC 1.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/installation)

Tutorial from cell ranger output to clustering (PBMC - RNA & ATAC) = https://satijalab.org/seurat/v4.0/weighted_nearest_neighbor_analysis.html



                ********** Pipeline implentation *********
                                *******
                      
***** Galaxy



***** NextFlow
https://github.com/WarrenLab/single-cell
https://figshare.com/articles/BICF_Cellranger_count_Analysis_Workflow/9702698
https://nf-co.re/scrnaseq/1.0.0
https://hub.docker.com/r/nfcore/demultiplex