Mercurial > repos > gaelcge > cellranger_atac_galaxy
comparison README.md @ 0:a62bafb1aaf8 draft default tip
"planemo upload commit ff0d185541dc4b0a5839fca166f1beb459dee61c"
| author | gaelcge |
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| date | Tue, 02 Aug 2022 19:42:44 +0000 |
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| 1 # GenAP2 Galaxy implementation of CellRanger-ATAC | |
| 2 Disclaimer: This wrapper for CellRanger-ATAC is not developed or supported by 10x Genomics. This wrapper was written by scientists at GenAP to help facilitate usage of CellRanger tools inside of Galaxy. | |
| 3 Please find the full, official 10x Genomics licensing information at : https://support.10xgenomics.com/docs/license. | |
| 4 | |
| 5 What is CellRanger ATAC? | |
| 6 | |
| 7 https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac | |
| 8 | |
| 9 Naming convention of FASTQ files internally in Galaxy follows thes guidelines: | |
| 10 | |
| 11 https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/using/fastq-input#rightname | |
| 12 | |
| 13 Installation: | |
| 14 1) Install this wrapper via the Galaxy toolshed. | |
| 15 2) CellRanger-ATAC (v2.0.0) is required for this wrapper and should be installed separately (see below). | |
| 16 | |
| 17 To use this tool, we assume that cellranger-atac (v.2.0.0) is available to Galaxy on the system, via the command cellranger-atac. Unfortunately at this point, we cannot include Cellranger-ATAC as part of this wrapper due to Licensing and distribution limitations. For more information on how to install CellRanger-ATAC on your system, please see : | |
| 18 https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/installation |