Graphing NGS data

Question

[n.joshi17]

I have Illumina reads from my NGS samples and I mapped them to a reference genome. Now I have mapped reads per chromosome and coverage data. How do I plot all chromosome coverage as one graph? i.e. a genome-wide coverage? Also, How can I plot coverage from multiple samples per chromosome on the same graph such that y-axis is the same? I am a beginner at NGS analysis.

Answer 1

[GenoMax]

Look at Qualimap to begin with for individual samples. MultiQC can then be used to aggregate multiple samples analyzed by Qualimap.