IGB normalisation of reads

Question

[shimbalama]

Hi there,

I've been tasked with visualising some RNAseq data (bacterial). I've been instructed to use IGB over IGV (which I'm more familiar with) as it can normalise the read counts so they are comparable. I've got my reference loaded with bams but I can't see any mention of a normalisation tool in the options/help pages. Have I been lead astray or am I missing something? I did DE with deseq2 so I have normalised counts per gene, but I'd like to plot at the base resolution.

Any help would be appreciated.

Regards, Liam

[Brian Bushnell]

I've been instructed to use IGB over IGV

Boo...

I like IGV and use it constantly. And yes, I've used it for visualization of bacterial RNA-seq data. I'd be interested in hearing anyone's comments on how/when IGB might be better.

Also, I would be very careful with automatic normalization. Normalization means you are not seeing the original data. It's not something I would trust to a visualization tool.

Answer 1

[Mason Meyer]

Hello shimbalama,

My name is Mason Meyer, Support Specialist for IGB. I apologize for the time it has taken me to respond to your post. You asked if IGB has a normalisation tool, and while IGB does not have a so-called "normalization tool" we may have a feature that can help in comparing your reads.

In IGB, you can create a Depth Graph from your read tracks. This depth graph is an overview of the relative density of annotation coverage across an entire chromosome (this is also known as a coverage graph). You can then adjust the Y-Axis Scale for the graphs and may want to set the Y-Axis Scale the same for both graph tracks when comparing. I have attached an image at the bottom of this post showing you an example of what I mean.

I am not an expert when it comes to normalisation, so I apologize if what I've mentioned does not help you. On the other hand, if you think it will help you, you may want to look at these two pages in our user's guide for specific instructions on generating graphs from annotation tracks and customizing graphs:

• Creating graph tracks from annotations tracks
• Graph (options and more info)

Also, if you have any other questions, please don't hesitate to ask me, or if you would like to share your files so that we can better assist you, feel free to contact us by using the links on our Support Page.

I am glad you have decided to give IGB a try. Many people find that they prefer IGB over other browsers due to its ease of use and smooth zooming/panning, and not to mention, IGB is packed with other convenient features that users want and need in a genome browser. Also, if you have any additional feature requests, our team is always eager to hear them so we can plan to add the feature in the near future. If you have any ideas, we would love to know about them!

Thanks again,

Mason Meyer IGB Support Specialist