bed

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

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.

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.

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

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