QualiMap

http://qualimap.conesalab.org/doc_html
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QualiMap provides a quality control analysis platform for high-throughput sequencing data, offering...
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### Example CRAN Repository for Ubuntu 10.04

Source: http://qualimap.conesalab.org/doc_html/intro.html

An example line to add to sources.list for installing R on Ubuntu 10.04 (Lucid) from a specific CRAN mirror.

```bash
deb http://cran.stat.ucla.edu/bin/linux/ubuntu lucid/
```

--------------------------------

### Qualimap BAM QC Example

Source: http://qualimap.conesalab.org/doc_html/command_line.html

A basic example of how to run Qualimap BAM QC analysis. The output directory will be automatically created if not specified.

```bash
qualimap bamqc -bam ERR089819.bam -c
```

--------------------------------

### Run BamQC with Output Directory

Source: http://qualimap.conesalab.org/doc_html/command_line.html

Example of running the 'bamqc' tool and specifying an output directory for the HTML report and raw data. Ensure the input BAM file is correctly specified.

```bash
qualimap bamqc -bam file.bam -outdir qualimap_results

```

--------------------------------

### Run Qualimap from Installation Directory

Source: http://qualimap.conesalab.org/doc_html/intro.html

Execute the Qualimap application by running the provided script from its installation directory. This is the primary method for launching Qualimap on Unix-like systems.

```bash
./qualimap
```

--------------------------------

### Example Qualimap RNA-seq Analysis Command

Source: http://qualimap.conesalab.org/doc_html/command_line.html

This is an example command to run RNA-seq QC analysis. It requires the input BAM file and GTF annotation file, and specifies an output directory.

```bash
qualimap rnaseq -bam kidney.bam -gtf human.64.gtf -outdir rnaseq_qc_results

```

--------------------------------

### Qualimap Counts QC Example

Source: http://qualimap.conesalab.org/doc_html/command_line.html

Example command to run Qualimap counts QC analysis. It specifies the input data file, enables comparison of conditions, sets the species to mouse, and defines the output directory. Ensure the input data file and counts file exist.

```bash
qualimap counts -d GlcN_countsqc_input.txt -c -s mouse -outdir glcn_mice_counts

```

--------------------------------

### Install OpenJDK 6 JRE on Ubuntu

Source: http://qualimap.conesalab.org/doc_html/intro.html

Install the OpenJDK 6 Java Runtime Environment on Ubuntu systems using the apt-get package manager.

```bash
sudo apt-get install openjdk-6-jre
```

--------------------------------

### Example Configuration File for Multi-sample BAM QC

Source: http://qualimap.conesalab.org/doc_html/command_line.html

Illustrates the format of the configuration file required by the -d argument. It specifies sample names, paths to BAM QC results or BAM files, and optionally sample conditions.

```text
sample_1	sample_1_stats	group_1
sample_2	sample_2_stats	group_1
sample_3	sample_3_stats	group_1
sample_4	sample_4_stats	group_2
sample_5	sample_5_stats	group_2
sample_6	sample_6_stats	group_2
```

--------------------------------

### Install Required R Packages Dependencies

Source: http://qualimap.conesalab.org/doc_html/intro.html

Install system-level libraries required by some R packages used by Qualimap, such as libxml2-dev and libcurl4-openssl-dev.

```bash
sudo apt-get install libxml2-dev
sudo apt-get install libcurl4-openssl-dev
```

--------------------------------

### Install Qualimap's R Dependencies using Script

Source: http://qualimap.conesalab.org/doc_html/intro.html

Execute the provided R script to automatically install all required R packages for Qualimap's advanced features. Ensure the QUALIMAP_HOME environment variable is set correctly.

```bash
sudo Rscript $QUALIMAP_HOME/scripts/installDependencies.r
```

--------------------------------

### Add CRAN Repository for R Installation on Ubuntu

Source: http://qualimap.conesalab.org/doc_html/intro.html

Add a CRAN mirror to the sources.list file to enable installation of the latest R version from public repositories on Ubuntu. Replace '<my.favorite.cran.mirror>' and '<name.of.your.distribution>' with appropriate values.

```bash
deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu <name.of.your.distribution>/
```

--------------------------------

### Install Qualimap's R Dependencies Manually

Source: http://qualimap.conesalab.org/doc_html/intro.html

Install R packages required by Qualimap manually. This is an alternative to using the installation script.

```r
install.packages("optparse")
# From Bioconductor
# source("http://bioconductor.org/biocLite.R")
# biocLite(c("NOISeq", "Repitools", "Rsamtools", "GenomicFeatures", "rtracklayer"))
```

--------------------------------

### Run BamQC with PDF Output File

Source: http://qualimap.conesalab.org/doc_html/command_line.html

Example demonstrating how to generate a PDF report for the 'bamqc' tool. The '-outfile' option specifies the name of the PDF report, while '-outdir' can still be used for raw data location.

```bash
qualimap bamqc -bam file.bam -outfile result.pdf

```

--------------------------------

### Run BamQC with Explicit PDF Output Format

Source: http://qualimap.conesalab.org/doc_html/command_line.html

Example showing how to explicitly set the output format to PDF using the '-outformat' option. The report will be saved in the specified output directory with a default name.

```bash
qualimap bamqc -bam file.bam -outdir qualimap_results -outformat pdf

```

--------------------------------

### Update Package List and Install R Core on Ubuntu

Source: http://qualimap.conesalab.org/doc_html/intro.html

After adding the CRAN repository, update the package list and install the R base core package on Ubuntu.

```bash
sudo apt-get update
sudo apt-get install r-base-core
```

--------------------------------

### Import Public Key for CRAN Mirror

Source: http://qualimap.conesalab.org/doc_html/intro.html

Import the public key for a CRAN mirror if it's not already present, which is necessary for secure package installation on Ubuntu.

```bash
gpg --keyserver subkeys.pgp.net --recv-key <required.key>
gpg -a --export <required.key> | sudo apt-key add -
```

--------------------------------

### Check R Version

Source: http://qualimap.conesalab.org/doc_html/intro.html

Verify the installed version of R using the Rscript command. Qualimap requires R version 3.1 or above.

```bash
Rscript --version
```

--------------------------------

### Running Qualimap Multi-BAMQC with a Configuration File

Source: http://qualimap.conesalab.org/doc_html/command_line.html

Demonstrates how to execute the qualimap multi-bamqc command using a specified input configuration file and output directory. Ensure the input file and directory exist.

```bash
unzip gh2ax_chip_seq.zip
cd gh2ax_chip_seq.txt
qualimap multi-bamqc -i gh2ax_chip_seq.txt -outdir gh2ax_multibamqc
```

--------------------------------

### Launch a QualiMap Tool

Source: http://qualimap.conesalab.org/doc_html/command_line.html

General command structure for launching any QualiMap analysis tool. Replace <tool_name> with the desired analysis (e.g., bamqc, rnaseq) and <tool_options> with specific parameters.

```bash
qualimap <tool_name> <tool_options>

```

--------------------------------

### Show Available QualiMap Tools

Source: http://qualimap.conesalab.org/doc_html/command_line.html

Use this command to list all available analysis tools within QualiMap and view their basic help information.

```bash
qualimap --help

```

--------------------------------

### Launch Qualimap on Windows

Source: http://qualimap.conesalab.org/doc_html/intro.html

Use the 'qualimap.bat' script to launch Qualimap on Microsoft Windows operating systems.

```bash
qualimap.bat
```

--------------------------------

### Qualimap multi-bamqc Command Usage

Source: http://qualimap.conesalab.org/doc_html/command_line.html

Displays the available options and arguments for the qualimap multi-bamqc command. Use this to understand the parameters for multi-sample BAM QC.

```bash
usage: qualimap multi-bamqc [-c] -d <arg> [-gff <arg>] [-hm <arg>] [-nr <arg>]
      [-nw <arg>] [-outdir <arg>] [-outfile <arg>] [-outformat <arg>] [-r]
-c,--paint-chromosome-limits   Only for -r mode. Paint chromosome limits inside
                               charts
-d,--data <arg>                File describing the input data. Format of the
                               file is a 2-column tab-delimited table.
                               Column 1: sample name
                               Column 2: either path to the BAM QC result or
                               path to BAM file (-r mode)
-gff,--feature-file <arg>      Only for -r mode. Feature file with regions of
                               interest in GFF/GTF or BED format
-hm <arg>                      Only for -r mode. Minimum size for a homopolymer
                               to be considered in indel analysis (default is
                               3)
-nr <arg>                      Only for -r mode. Number of reads analyzed in a
                               chunk (default is 1000)
-nw <arg>                      Only for -r mode. Number of windows (default is
                               400)
-outdir <arg>                  Output folder for HTML report and raw data.
-outfile <arg>                 Output file for PDF report (default value is
                               report.pdf).
-outformat <arg>               Format of the ouput report (PDF or HTML, default
                               is HTML).
-r,--run-bamqc                 Raw BAM files are provided as input. If this
                               option is activated BAM QC process first will be
                               run for each sample, then multi-sample analysis
                               will be performed.

```

--------------------------------

### Qualimap RNA-seq Command Line Usage

Source: http://qualimap.conesalab.org/doc_html/command_line.html

This displays the available options for the `qualimap rnaseq` command. Use this to understand parameter choices for RNA-seq QC analysis.

```bash
usage: qualimap rnaseq [-a <arg>] -bam <arg> -gtf <arg> [-oc <arg>] [-outdir
      <arg>] [-outfile <arg>] [-outformat <arg>] [-p <arg>]
-a,--algorithm <arg>             Counting algorithm:
                                 uniquely-mapped-reads(default) or
                                 proportional.
-bam <arg>                       Input mapping file in BAM format.
-gtf <arg>                       Annotations file in Ensembl GTF format.
-npb,--num-pr-bases <arg>        Number of upstream/downstream nucleotide bases
                                 to compute 5'-3' bias (default is 100).
-ntb,--num-tr-bias <arg>         Number of top highly expressed transcripts to
                                 compute 5'-3' bias (default is 1000).
-oc <arg>                        Path to output computed counts.
-outdir <arg>                    Output folder for HTML report and raw data.
-outfile <arg>                   Output file for PDF report (default value is
                                 report.pdf).
-outformat <arg>                 Format of the ouput report (PDF or HTML, default is HTML).
-p,--sequencing-protocol <arg>   Sequencing library protocol:
                                 strand-specific-forward,
                                 strand-specific-reverse or non-strand-specific
                                 (default)
-pe,--paired                     Setting this flag for paired-end experiments
                                 will result in counting fragments instead of
                                 reads.
-s,--sorted                      This flag indicates that the input file is
                                 already sorted by name. If not set, additional
                                 sorting by name will be performed. Only
                                 required for paired-end analysis.

```

--------------------------------

### Qualimap BAM QC Usage

Source: http://qualimap.conesalab.org/doc_html/command_line.html

This displays the usage information for the qualimap bamqc command, listing all available options and their descriptions. The -bam option is the only required parameter.

```bash
usage: qualimap bamqc -bam <arg> [-c] [-gd <arg>] [-gff <arg>] [-hm <arg>] [-nr
   <arg>] [-nt <arg>] [-nw <arg>] [-oc <arg>] [-os] [-outdir <arg>]
   [-outfile <arg>] [-outformat <arg>] [-p <arg>]
-bam <arg>                           Input mapping file in BAM format
-c,--paint-chromosome-limits         Paint chromosome limits inside charts
-cl,--cov-hist-lim <arg>             Upstream limit for targeted per-bin
                                  coverage histogram (default is 50X)
-dl,--dup-rate-lim <arg>             Upstream limit for duplication rate
                                  historgram (default is 50)
-gd,--genome-gc-distr <arg>          Species to compare with genome GC
                                  distribution. Possible values: HUMAN or
                                  MOUSE.
-gff,--feature-file <arg>            Feature file with regions of interest in
                                  GFF/GTF or BED format
-hm <arg>                            Minimum size for a homopolymer to be
                                  considered in indel analysis (default is
                                  3)
-ip,--collect-overlap-pairs          Activate this option to collect statistics
                                  of overlapping paired-end reads
-nr <arg>                            Number of reads analyzed in a chunk
                                  (default is 1000)
-nt <arg>                            Number of threads (default is 8)
-nw <arg>                            Number of windows (default is 400)
-oc,--output-genome-coverage <arg>   File to save per base non-zero coverage.                                  Warning: large files are  expected for large
                                  genomes
-os,--outside-stats                  Report information for the regions outside
                                  those defined by feature-file  (ignored
                                  when -gff option is not set)
-outdir <arg>                        Output folder for HTML report and raw
                                  data.
-outfile <arg>                       Output file for PDF report (default value
                                  is report.pdf).
-outformat <arg>                     Format of the ouput report (PDF or HTML,
                                  default is HTML).
-p,--sequencing-protocol <arg>       Sequencing library protocol:
                                  strand-specific-forward,
                                  strand-specific-reverse or
                                  non-strand-specific (default)
-sd,--skip-duplicated             Activate this option to skip duplicate
                                  alignments from the analysis. If the
                                  duplicates are not flagged in BAM file,
                                  then they will be detected by Qualimap
                                  and can be selected for skipping.
-sdmode,--skip-dup-mode <arg>        Specific type of duplicated alignments to
                                  skip (if this option is activated).
                                  0 : only flagged duplicates (default)
                                  1 : only estimated by Qualimap
                                  2 : both flagged and estimated
```

--------------------------------

### Enable Headless Java Mode

Source: http://qualimap.conesalab.org/doc_html/faq.html

Disable the X11 display requirement for Java by setting the -Djava.awt.headless=true option. This can be done by modifying the java_options variable in the qualimap script or by setting the JAVA_OPTS environment variable.

```bash
java_options="-Djava.awt.headless=true -Xmx$JAVA_MEM_SIZE -XX:MaxPermSize=1024m"
```

--------------------------------

### Common QualiMap Command Line Options

Source: http://qualimap.conesalab.org/doc_html/command_line.html

These options are applicable to most QualiMap command line tools for configuring output. They control the output directory, PDF report filename, and report format.

```bash
-outdir <arg>                        Output folder for HTML report and raw
                                      data.
-outfile <arg>                       Output file for PDF report (default value
                                     is report.pdf).
-outformat <arg>                     Format of the ouput report (PDF or HTML,
                                      default is HTML).

```

--------------------------------

### Qualimap Counts QC Usage

Source: http://qualimap.conesalab.org/doc_html/command_line.html

Displays the usage information for the qualimap counts command, outlining available options and their descriptions. Use this to understand the parameters required for the analysis.

```bash
usage: qualimap counts [-c] -d <arg> [-i <arg>] [-k <arg>] [-outdir <arg>]
      [-outfile <arg>] [-outformat <arg>] [-R <arg>] [-s <arg>]
-c,--compare             Perform comparison of conditions. Currently 2 maximum
                         is possible.
-d,--data <arg>          File describing the input data. Format of the file is
                         a 4 column tab-delimited table.
                         Column 1: sample name
                         Column 2: condition of the sample
                         Column 3: path to the counts data for the sample
                         Column 4: index of the column with counts
-i,--info <arg>          Path to info file containing genes GC-content, length
                         and type.
-k,--threshold <arg>     Threshold for the number of counts
-outdir <arg>            Output folder for HTML report and raw data.
-outfile <arg>           Output file for PDF report (default value is
                         report.pdf).
-outformat <arg>         Format of the ouput report (PDF or HTML, default is
                         HTML).
-R,--rscriptpath <arg>   Path to Rscript executable (by default it is assumed
                         to be available from system $PATH)
-s,--species <arg>       Use built-in info file for the given species: HUMAN or
                         MOUSE.

```

--------------------------------

### Unset DISPLAY Environment Variable

Source: http://qualimap.conesalab.org/doc_html/faq.html

If encountering 'Can't connect to X11 window server' errors, unset the DISPLAY environment variable to allow Qualimap to run without a graphical display.

```bash
unset DISPLAY
```

```bash
export DISPLAY=:0
```

--------------------------------

### Qualimap Clustering Command Usage

Source: http://qualimap.conesalab.org/doc_html/command_line.html

Use this command to perform clustering of epigenomic signals. Specify sample BAM files, control BAM files, and a regions file.

```bash
usage: qualimap clustering [-b <arg>] [-c <arg>] -control <arg> [-expr <arg>]
       [-f <arg>] [-l <arg>] [-name <arg>] [-outdir <arg>] [-outformat <arg>]
       [-r <arg>] -regions <arg> -sample <arg> [-viz <arg>]
 -b,--bin-size <arg>          size of the bin (default is 100)
 -c,--clusters <arg>          comma-separated list of cluster sizes
 -control <arg>               comma-separated list of control BAM files
 -expr <arg>                  name of the experiment
 -f,--fragment-length <arg>   smoothing length of a fragment
 -l <arg>                     upstream offset (default is 2000)
 -name <arg>                  comma-separated names of the replicates
 -outdir <arg>                output folder
 -outformat <arg>             output report format (PDF or HTML, default is
                              HTML)
 -r <arg>                     downstream offset (default is 500)
 -regions <arg>               path to regions file
 -sample <arg>                comma-separated list of sample BAM files
 -viz <arg>                   visualization type: heatmap or line
```

```bash
qualimap clustering -sample clustering/hmeDIP.bam -control clustering/input.bam -regions annotations/transcripts.human.64.bed -outdir clustering_result
```

--------------------------------

### Qualimap Compute Counts Command Usage

Source: http://qualimap.conesalab.org/doc_html/command_line.html

Use this command to compute counts from mapping data. Requires a BAM file and a GTF/GFF/BED file.

```bash
usage: qualimap comp-counts [-a <arg>] -bam <arg> -gtf <arg> [-id <arg>] [-out
      <arg>] [-p <arg>] [-pe] [-s <arg>] [-type <arg>]
-a,--algorithm <arg>             Counting algorithm:
                                 uniquely-mapped-reads(default) or proportional
-bam <arg>                       Mapping file in BAM format
-gtf <arg>                       Region file in GTF, GFF or BED format. If GTF
                                 format is provided, counting is based on
                                 attributes, otherwise based on feature name
-id <arg>                        GTF-specific. Attribute of the GTF to be used
                                 as feature ID. Regions with the same ID will
                                 be aggregated as part of the same feature.
                                 Default: gene_id.
-out <arg>                       Path to output file
-p,--sequencing-protocol <arg>   Sequencing library protocol:
                                 strand-specific-forward,
                                 strand-specific-reverse or non-strand-specific
                                 (default)
-pe,--paired                     Setting this flag for paired-end experiments
                                 will result in counting fragments instead of
                                 reads
-s,--sorted <arg>                This flag indicates that the input file is
                                 already sorted by name. If not set, additional
                                 sorting by name will be performed. Only
                                 required for paired-end analysis.
-type <arg>                      GTF-specific. Value of the third column of the
                                 GTF considered for counting. Other types will
                                 be ignored. Default: exon
```

```bash
qualimap comp-counts -bam kidney.bam -gtf ../annotations/human.64.gtf  -out kidney.counts
```

--------------------------------

### Set Java Heap Memory Size

Source: http://qualimap.conesalab.org/doc_html/faq.html

Increase the maximum Java heap memory size for Qualimap using the --java-mem-size argument. Ensure there is no whitespace between the argument and its value.

```bash
qualimap --java-mem-size=1200M
```

```bash
qualimap bamqc -bam very_large_alignment.bam --java-mem-size=4G
```

--------------------------------

### Modify Default Java Memory Size

Source: http://qualimap.conesalab.org/doc_html/faq.html

Change the default Java memory size by editing the JAVA_MEM_DEFAULT_SIZE variable in the Qualimap launching script.

```bash
JAVA_MEM_DEFAULT_SIZE=”1200M”
```
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