Difference between revisions of "CellRanger"
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[[Category:Software]][[Category:Biology]][[Category:Bioinformatics]][[Category:NGS]][[Category:RNA-Seq]] | [[Category:Software]][[Category:Biology]][[Category:Bioinformatics]][[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--> | ||
| − | == | + | ==Required Modules== |
| − | + | ===Serial=== | |
| + | * {{#var:app}} | ||
| + | <!-- | ||
| + | ===Parallel (OpenMP)=== | ||
| + | * intel | ||
| + | * {{#var:app}} | ||
| + | ===Parallel (MPI)=== | ||
| + | * intel | ||
| + | * openmpi | ||
| + | * {{#var:app}} | ||
| + | --> | ||
==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. | |
|}} | |}} | ||
Revision as of 18:58, 26 May 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.
Required Modules
Serial
- cellranger
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.