Command Line Interface

General Description

Each analysis type presented in QualiMap GUI is also available as command line tool. The common pattern to launch the tool is the following:

qualimap <tool_name> <tool_options>

<tool_name> is the name of the desired analysis. This could be: bamqc, countsqc, clustering or counts.

<tool_options> are specific to each type analysis. If not option is provided for the specific tool a full list of available options will be shown

Note

If you are using Qualimap on Unix server without X11 system, make sure that the DISPLAY environment variable is unset. Otherwise this might result in problems when running Qualimap. Here is an instruction how to solve this issue.

To show available tools use command:

qualimap --help

BAM QC

The following command allows to perform BAM QC analysis:

usage: qualimap bamqc -bam <arg> [-c] [-gd <arg>] [-gff <arg>] [-nr <arg>] [-nt
       <arg>] [-nw <arg>] [-os] [-outdir <arg>] [-outformat <arg>]
 -bam <arg>                     input mapping file
 -c,--paint-chromosome-limits   paint chromosome limits inside charts
 -gd <arg>                      compare with genome distribution (possible
                                values: HUMAN or MOUSE)
 -gff <arg>                     region file (in GFF/GTF or BED format)
 -hm <arg>                      minimum size for a homopolymer to be considered
                                in indel analysis (default is 3)
 -nr <arg>                      number of reads in the chunk (default is 500)
 -nt <arg>                      number of threads (default equals the number of cores)
 -nw <arg>                      number of windows (default is 400)
 -os,--outside-stats            compute region outside stats (only with -gff
                                option)
 -outdir <arg>                  output folder
 -outformat <arg>               output report format (PDF or HTML, default is
                                HTML)
 -p <arg>                       specify protocol to calculate correct strand
                                reads (works only with -gff option, possible
                                values are STRAND-SPECIFIC-FORWARD or
                                STRAND-SPECIFIC-REVERSE, default is
                                NON-STRAND-SPECIFIC)

The only required parameter is bam – the input mapping file.

If outdir is not provided, it will be created automatically in the same folder where BAM file is located.

Detailed explanation of available options can be found here.

Example (data available here):

qualimap bamqc -bam ERR089819.bam -c

Counts QC

To perform counts QC analysis (evaluation of RNA-seq data) use the following command:

usage: qualimap counts -d1 <arg> [-d2 <arg>] [-i <arg>] [-k <arg>] [-n1 <arg>]
       [-n2 <arg>] [-outdir <arg>] [-outformat <arg>] [-s <arg>]
 -d1,--data1 <arg>      first file with counts
 -d2,--data2 <arg>      second file with counts
 -i,--info <arg>        info file
 -k,--threshold <arg>   threshold for the number of counts
 -n1,--name1 <arg>      name for the first sample
 -n2,--name2 <arg>      name for second sample
 -outdir <arg>          output folder
 -outformat <arg>       output report format (PDF or HTML, default is HTML)
 -s,--species <arg>     use default file for the given species [human | mouse]

Detailed explanation of available options can be found here.

Example (data available here):

qualimap counts -d1 kidney.counts -d2 liver.counts -s human -outdir results

Clustering

To perform clustering of epigenomic signals use the following command:

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

Detailed explanation of available options can be found here.

Example (data available here):

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

Compute counts

To compute counts from mapping data use the following command:

usage: qualimap comp-counts [-algorithm <arg>] -bam <arg> -gtf <arg> [-id <arg>]
       [-out <arg>] [-protocol <arg>] [-type <arg>]
 -algorithm <arg>   uniquely-mapped-reads(default) or proportional
 -b                 calculate 5' and 3' coverage bias
 -bam <arg>         mapping file in BAM format)
 -gtf <arg>         region file in GTF format
 -id <arg>          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
 -protocol <arg>    forward-stranded,reverse-stranded or non-strand-specific
 -type <arg>        Value of the third column of the GTF considered for
                    counting. Other types will be ignored. Default: exon

Detailed explanation of available options can be found here.

Example (data available here):

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