bioinfoipec/qualimap repository overview

⁠Qualimap

This image facilitates the usage of QualiMap⁠, a platform-independent application to facilitate the quality control of alignment sequencing data.

⁠Using the QualiMap image

Supported types of experiments include:

• Whole-genome sequencing.
• Whole-exome sequencing.
• RNA-seq.
• ChIP-seq.

By running the command docker run --rm -v /your/data/dir:/data bioinfoipec/qualimap qualimap -h you can list the tools included in this suite, namely:

• 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.

To obtain the help of a particular tool, you just need to run: docker run --rm -v /your/data/dir:/data bioinfoipec/qualimap qualimap <tools> (e.g. docker run --rm -v /your/data/dir:/data bioinfoipec/qualimap qualimap bamqc)

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data bioinfoipec/qualimap qualimap <tools> <options>

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input file you want to analyze.
• <tools> to the name of the QualiMap tool you want to use.
• <options> with the specific options of the QualiMap tool. These options will include the input/output files, which should be referenced under /data/.

For instance, to use the bamqc tool with HG00096.chrom20.bam alignment with 400 windows and size of a homopolymer = 3, you should run: docker run --rm -v /your/data/dir:/data bioinfoipec/qualimap qualimap bamqc -bam /data/HG00096.chrom20.bam -c -nw 400 -hm 3

⁠Test data

To test the previous command, the sequence alignment file used is available here⁠.