Difference between revisions of "CellRanger"
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(Created page with "Category:SoftwareCategory:BiologyCategory:BioinformaticsCategory:NGSRNA-Seq {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|CellRanger}} |{{#vardefine:u...") |
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| − | [[Category:Software]][[Category:Biology]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:RNA-Seq]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
| − | |{{#vardefine:app| | + | |{{#vardefine:app|cellranger}} |
|{{#vardefine:url|https://support.10xgenomics.com/single-cell/software/pipelines/latest/what-is-cell-ranger}} | |{{#vardefine:url|https://support.10xgenomics.com/single-cell/software/pipelines/latest/what-is-cell-ranger}} | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | Cell Ranger is a set of analysis pipelines that | + | Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3 RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 supports libraries generated by the Chromium Single Cell 3' v1 and v2 reagent kits. |
<!--Modules--> | <!--Modules--> | ||
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_REF - reference data directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | Reference datasets can be found in the directory accessible via $HPC_CELLRANGER_REF variable. | |
|}} | |}} | ||
Latest revision as of 18:24, 12 August 2022
Description
Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3 RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 supports libraries generated by the Chromium Single Cell 3' v1 and v2 reagent kits.
Environment Modules
Run module spider cellranger to find out what environment modules are available for this application.
System Variables
- HPC_CELLRANGER_DIR - installation directory
- HPC_CELLRANGER_REF - reference data directory
Additional Information
Reference datasets can be found in the directory accessible via $HPC_CELLRANGER_REF variable.