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:

In order to help you as quickly as possible, make sure to include the following information:

  • Which version of GV are you running?
  • What operating system? OS X, Windows, ...?
  • Which version of Java are you running?
  • If you have problems with specific files, it is extremely helpful if you can share to files for us to reproduce the problem. Are those files local or remote?
  • Include the log file from the problematic GenomeView run. Instructions to find log files can be found here:
    http://www.genomeview.org/content/where-do-i-find-log-files

If you discover a bug or you have a feature request, please log a ticket on the bug tracker.

What extension should the tab-delimited pileup have?

Answer: 

For general instructions on preparing the pileup format
http://genomeview.org/content/preparing-pileup

For the tab delimited file, you should include .swig somewhere in the filename.

We typically end up with something like:
bigfile.bam.swig.bgz

Why do the high-mem webstarts not work?

Answer: 

The high-mem webstarts only work on 64 bit machines with sufficient memory. The error you receive is because Java was unable to allocate the requested memory.

1) Either because you don't have that much memory.

2) 32-bit Java on Windows can only allocate up to 1.2gb reliably, it may work up to 2 or 3 gb on Linux/mac os 32 bit. On the latter two I'm uncertain of the exact limits.

Feature indexing fails - Tabix segmentation fault

Answer: 

We have identified issues that can result in tabix giving a segmentation fault.

1) Tabix does not support the UCSC header line. You'll have to remove this line
track name=blabalh description="more blah blah"

2) Columns in a bed/gff file must be seperated with tab characters, not with regular spaces. Tabix will give a segmentation fault when trying to index a file with spaces instead of tabs.

3) There should be no comment lines (lines starting with #) in the bed/gff file.

4) There should be no empty lines, or lines with only white spaces.

I can not scroll or navigate in my data!

Answer: 

When you only load features or sequence read alignments (BAM files). GenomeView cannot know how long the reference sequence is and will not enable you to browse around.

This is easily solved by loading the reference sequence from a fasta file (indexed if it's a large one) or from the Genome Explorer (File > Show Genome Explorer).

Is there a way to export data from GenomeView?

Answer: 

Annotation can be exported using 'File' > 'Save annotation'

All other data can be exported using 'File' > 'Export data'

Where did the pileup/SNP track go with my BAM file?

Answer: 

In a recent version of GenomeView (1255+) we had to split the functionality of the pileup/SNP track and the short read track which shows the individual reads.

Essentially, the pileup was calculated in real-time, but this proved to be impractical for very large data sets. Therefore we now support the pile-up format from samtools, which has the pile-up and SNP functionality.

The pile-up track is described GUI section in the manual.

When I add 2 annotations in BED format, the 2 annotations collapse into 1 line.

Answer: 

With BED files this is a bit tricky, but possible. We typically use GFF files, where you have a dedicated field for the type of feature.

In BED you can add the following line at the top of your bed file, this will let GenomeView know how to name the track.

track name=Name_of_your_data_without_spaces

You can configure the color of each track in File > Configuration > Feature track

Is there any sample data available?

Answer: 

There sure is. We offer example instances pre-loaded with a bunch of public data over in the demo section.

We also have the genomes sections, which offers for a limited set of genomes the reference sequence and the reference annotation. If you want another genome there, let us know and we'll put it up.

Where are the configuration and plugin directory of GenomeView?

Answer: 

The GenomeView configuration directory, this directory is named .genomeview and resides in your home directory. On a *nix system your home directory is typically located at /home/username. On Window XP it is found at C:\Documents and Settings\username.

If you have trouble finding this directory, you can start GenomeView, goto to the 'Help' menu and click 'About'. Near the bottom of that dialog it shows the path where to find the configuration file.

Where do I change which data types I see in the reading frames?

Answer: 

At the moment only annotation features of the type "CDS" can be displayed in the reading frame of the structure track.

It used to be so that any type could be displayed and it will be done as part of ticket 3166236

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