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Support - Frequently asked questions

This section of the documentation tries to address a number of common and less common issues you can come across while working with GenomeView.

If your problem is not addressed here, please:

We are happy to help you.

Where do I find documentation?

Fri, 08/19/2011 - 00:49 — Thomas Abeel
Answer: 

This list does not cover all topics, but should cover the most common ones. The menu on the left with the title 'Documentation' has links to all manual pages.

Why doesn't GenomeView correctly detect my BED file?

Wed, 08/03/2011 - 21:26 — Thomas Abeel
Answer: 

The pop-up message means that GenomeView cannot detect the file format automatically. The BED file format is particularly finicky, because the specification is pretty broad on what's allowed, which in some cases conflicts with other file formats.

For a BED file to be automatically recognized as such, it needs to contain all 12 fields.
http://genome.ucsc.edu/FAQ/FAQformat.html#format1

How do I fix the order of the tracks in an integrated GenomeView instance?

Tue, 07/26/2011 - 23:50 — Thomas Abeel
Answer: 

You can fix the order in which the tracks appear in the configuration file that you supply to the GenomeView instance.

Add lines of the following type to the configuration file to have the gene, mRNA and CDS annotation tracks near the top.

track:weight:gene=1
track:weight:mRNA=2
track:weight:CDS=3

The higher the weight, the lower the track will be displayed.

Tracks that do not have an explicit weight set in the configuration file, will receive one starting at 1000.

How do I integrate GenomeView in my website?

Tue, 07/26/2011 - 17:35 — Thomas Abeel
Answer: 

Preloading data in GenomeView can be done in several ways and depends on whether you are using the webstart version or the applet version.

Both methods are explained in detail in the integration manual page.

If you are interested in integrating GenomeView as an editor, check out the editor integration page.

I'm getting "Max stacking depth reached", how do I see my other reads?

Tue, 07/12/2011 - 21:20 — Thomas Abeel
Answer: 

This is due to the high read depth.

By default the maximum depth that reads will be stacked is 50. You can change this behavior in the configuration panel:

File > configuration > short reads

Change the number in the box 'Maximum display depth of stacked reads...' to a higher number. This box is half-way down the screen.

When I load a sorted bamfile and a fasta file, should I automatically see the coverage graph and SNP call track?

Mon, 06/27/2011 - 15:38 — Thomas Abeel
Answer: 

No, the coverage and SNP are in a separate data file.

Instructions to create this file:
http://genomeview.org/content/preparing-pileup

There are two recommended file formats depending on your visualization needs:

1) TDF: this file format is the most space efficient and fastests, however, it only has coverage information.
see the TDF section in the link above

On Mac OS X, why does it crash, hang, kill my browser ?

Mon, 04/18/2011 - 15:51 — Thomas Abeel
Answer: 

The Java support Apple provides is different from other platforms, which makes using Java on a Mac a bit more challenging.

Some things that you can do to improve the situation.

1) Install Java 6 from Oracle.

2) Run Java in a separate process from your web browser.

You may be interested in the instructions to run GenomeView on a Mac.

How do I reorder the species in a multiple alignment?

Thu, 04/14/2011 - 01:31 — Thomas Abeel
Answer: 

Right click on the multiple alignment track visualization and there should be a menu that has an item which allows you to reorder ("Rearrange order") them. This can be done by dragging the names of the species up and down in the window that pops up when you click the "Rearrange order" menu item.

Why do I get BED features outside the sequence when I'm loading a fasta file with fai index?

Tue, 03/08/2011 - 17:38 — Thomas Abeel
Answer: 

The most likely problem is that you accidentally loaded the fasta file AND the fasta.fai file. You do not have to load the index manually, GenomeView will treat is as a separate data source, hence the bed features popping up.

When you only load the fasta file, GenomeView will use the index for fast access, but you won't get the weird additional BED features.

Is there any way to make sure that the vertical scales for multiple sequencing lanes match in the pile up track?

Mon, 03/07/2011 - 16:44 — Thomas Abeel
Answer: 

Goto 'File'> 'Configuration' > 'Pile up tracks'

Set the maximum height to whatever you want it to be.

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