Qualimap Large Standard Deviation

[shmibble]

Hi,

I'm using Qualimap for quality control in a pipeline.
Under "Coverage" I get a standard deviation that is larger than the mean value. This seems a little suspicious. Does this mean there is likely some sort of problem?

Thanks for the help

[Brian Bushnell]

I've never used Qualimap, but it's not unusual to have a standard deviation larger than the mean, depending on your experiment. Particularly with single-cell, or LMP libraries, or anything over-amplified, or other protocols that are expected to be highly biased. Can you give more details?

[shmibble]

Thanks for the reply.
I am amplifying certain areas more than others. So that might be the issue.
As I am still no expert in this, What would you recommend other than Qualimap?

[Brian Bushnell]

Before I can recommend something, I'd need to know exactly what you're trying to measure. BBMap can generate the standard deviation and average coverage, but there's no reason to expect it would give a different answer. You are running an experiment with intentionally uneven coverage, so when you analyze the coverage and find that it is uneven, that should be what you expect.

[shmibble]

You're right. I guess I didn't think about that before. I don't really need a different program then.

Thanks!