Question: Is There An Alternative For Igb Which Can Display Normalized Rna-Seq Coverages?
7
gravatar for Konrad
9.9 years ago by
Konrad690
Germany
Konrad690 wrote:

For a comparative view on RNA-Seq data from different conditions we use the Integrated Genome Browser (IGB) currently. To do so we translate the read mapping output to GR files - a very lightweight format with two columns: one for the position of a nucleotide, one for the coverage value of it. The advantage of this approach is that the coverage values can be normalized during the GR-file creation (e.g. to the number of mapped reads of each probe) which makes a comparison of different samples possible.

The problem is that the IGB is rather slow so I would like to know if there is any other genome browser that can either handle the mentioned GR files or is able to normalize/rescale the shown coverages. It should be quicker than IGB (to load and to handle - I guess this kills most of the web based genome browsers like GBrowse/GBrowse2) and open-source licensed.

Maybe I am wrong but obvious candidates like IGV or Gaggle seems to lack the normalization feature.

Can anyone suggest a genome browser which fulfills the admittedly long wish list?

PS: I am aware of the similar question but my precise problem is not covered there.

ADD COMMENTlink written 9.9 years ago by Konrad690
7
gravatar for Aaron Statham
9.9 years ago by
Aaron Statham1.1k
Australia
Aaron Statham1.1k wrote:

Wiggle files are almost as simple as .gr files, and can be loaded into IGV

ADD COMMENTlink written 9.9 years ago by Aaron Statham1.1k

Thanks, Aaron. I thought it might work without changing the format. But it looks like WIG is the more commonly used one.

ADD REPLYlink written 9.9 years ago by Konrad690

IGV 2.0 beta have more capabilities to handle RNA-seq data and new file formats (vcf, cufflinks, GWAS, goby, gtf, custom file formats too)

ADD REPLYlink written 9.8 years ago by Rm8.0k
2
gravatar for Lance
9.9 years ago by
Lance30
United States
Lance30 wrote:

One option would be SeqMonk. It is more of an analysis tool than a genome browser, but it might be useful for the sort of thing you are doing. You basically define a set of probes (by importing a GFF file for example) and then calculate statistics on those probes. It has various options for normalization, etc.

ADD COMMENTlink written 9.9 years ago by Lance30

Indeed. Judging from the screenshots this seems to be a quite powerful tool for such purposes. I will test how well it performs. Thanks, Lance!

ADD REPLYlink written 9.9 years ago by Konrad690
1
gravatar for Ann
9.8 years ago by
Ann2.3k
Concord NC USA
Ann2.3k wrote:

Hello,

Thank you for the question....

IGB can also display files in bedGraph (wig) format.

Forgive me if I misunderstand your goals, but for what you're doing, I would strongly recommend using a bedGraph format, which will allow you to visualize values associated with regions instead of values associated with individual bases.

For example, let's say your probe (inferred from the RNA-Seq data and gene models?) corresponds to an exonic region on chr1, coordinates 1 to 100. Let's also say your normalized read count is 100.5.

To represent this data point, your bedGraph file would look like this:

chr1 1 100 100.5

A non-normalized bedGraph file calculated from simple read coverage might have many millions of such regions, but your normalization procedure should cut down on the total number of data points. So I think IGB should not have too many problems rendering your normalized files if you convert them to bedGraph. Also, it might be a better format for your goals, because you would be able to quickly recognize if your probe detection procedure is working as expected. However, IGB will also support incremental data loading, which means that you should be able to load many different files covering your regions of interest. This is very useful when making figures for papers and slides, because then you can build a very rich data scene without having to load massive amounts of data at once.

Very best wishes,

Ann Loraine

ADD COMMENTlink written 9.8 years ago by Ann2.3k
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