Difference between revisions of "QualiMap"

Revision as of 13:35, 12 October 2015

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.

Required Modules

Serial

qualimap

System Variables

HPC_{{#uppercase: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:

Konstantin Okonechnikov, Ana Conesa and Fernando García-Alcalde "Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data." Bioinformatics(2015)

@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 43: / Line 43: @@
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+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
 |}}