QualiMap v.2.3
Built on 2023-05-19 16:57

usage: qualimap <tool> [options]

To launch GUI leave <tool> empty.

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

Special arguments: 

    --java-mem-size  Use this argument to set Java memory heap size. Example:
                     qualimap bamqc -bam very_large_alignment.bam --java-mem-size=4G
                     
usage: qualimap rnaseq [-a <arg>] -bam <arg> -gtf <arg> [-npb <arg>] [-ntb
       <arg>] [-oc <arg>] [-outdir <arg>] [-outfile <arg>] [-outformat <arg>]
       [-p <arg>] [-pe] [-s]
 -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>                        Output file for computed counts. If only name
                                  of the file is provided, then the file will be
                                  saved in the output folder.
 -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 output report (PDF, HTML or both
                                  PDF: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.