Difference between revisions of "QualiMap"
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| − | [[Category:Software]][[Category:Biology]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Alignment]] |
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| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation 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== | ||
| − | + | Available tools: | |
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| + | *bamqc - Evaluate NGS mapping to a reference genome | ||
| + | *rnaseq - Evaluate RNA-seq alignment data | ||
| + | *counts - Counts data analysis (further RNA-seq data evaluation) | ||
| + | *multi-bamqc - Compare QC reports from multiple NGS mappings | ||
| + | *clustering - Cluster epigenomic signals | ||
| + | *comp-counts - Compute feature counts | ||
|}} | |}} | ||
Latest revision as of 19:32, 24 August 2022
Description
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
Environment Modules
Run module spider qualimap to find out what environment modules are available for this application.
System Variables
- HPC_QUALIMAP_DIR - installation directory
Additional Information
Available tools:
- bamqc - Evaluate NGS mapping to a reference genome
- rnaseq - Evaluate RNA-seq alignment data
- counts - Counts data analysis (further RNA-seq data evaluation)
- multi-bamqc - Compare QC reports from multiple NGS mappings
- clustering - Cluster epigenomic signals
- comp-counts - Compute feature counts
Citation
If you publish research that uses qualimap you have to cite it as follows: