How to create coverage graph/plot for an entire Illumina run

Question

[SaltedPork]

Hi

I have BAM files with my reads aligned to a reference (This is covid data btw) Is there a program/tool that can plot the coverage for each run? With genome position on x axis and read count on y axis.

I already have graphs for each sample, I want to avergae each position and plot for an entire run.

[Amitm]

Hi, One solution would be to convert your BAMs into bigWig format files which can then be visualised in IGV. Refer to deeptools bamCoverage for one way to do that. There are other tools in the suite that can take multiple bigWig files to produce summary plots.You would probably need some tinkering to create what you want. But visualising bigWig files on IGV should be straightforward.

[GenoMax]

I want to avergae each position and plot for an entire run.

In that case you could merge the BAM files using samtools merge and then use qualimap (LINK) on the merged data file.