IGB- genome sequence in sequence viewer just shows dashes

Question

[cory.culligan]

Hello,

I am using IGB V8.0.1 I am loading the Sorghum bicolor Sbicolor_255_v2.1.gene_exons.gff3 and Sbicolor_255_v2.0.fa

that I downloaded from Phytozome V10. When I right click on my gene of interest, and select "view genomic sequence in sequence viewer" I shows only dashed (no nucleotides). The strange thing is that the color code for introns/exons is shown and the start and stop sites are annotated. I have tried re-downloading the files from Phytozome and it did not help. My Arabidopsis and the V1.0 Sorghum GFF2 files work just fine and show the sequence for any gene I try. Can anyone give me advice on how to solve this problem.

Thanks in advance,

Cory

Answer 1

[Nowlan Freese]

Hi Cory,

Try updating your IGB to version 8.1.12 - latest release.

I tried to reproduce what you're seeing, but it works correctly for me - I can view the genomic sequence in the sequence viewer.

Here's a description of what I did to try and reproduce it using IGB version 8.1.12:

1. Selected File > Open Custom Genome
2. Selected Sbicolor_255_v2.0.fa file (uncompressed) as the reference sequence
3. Selected File > Open and selected Sbicolor_255_v2.1.gene_exons.gff3
4. Clicked the Load Data button to load all of the gene models on Chr01
5. Zoomed in on a gene model
6. Right-clicked the gene model and selected View Genomic Sequence in Sequence Viewer

The sequence viewer appeared with the correct sequence and intron/exon color code.

IGBQuickLoad contains the Sorghum bicolor v1.0. genome assembly but not the 2.0 assembly. If it would help, we can add the v2.0 assembly. If we do this, you won't need to load it as a custom genome - it will appears as one of the options in the Current Genome tab and will load automatically when you click the Sorghum image on the IGB start screen.

Let me know if this helps!

Answer 2

[Ann]

A follow-up:

We added Sorghum genome (version 2.0 assembl) plus gene annotations to IGBQuickLoad.

See:

• New genome directory for Sorghum on IGBQuickLoad.org - http://igbquickload.org/quickload/S_bicolor_Jun_2013/
• Blog post describing how we re-formatted the data from Phytozome: http://lorainelab.org/?p=513

To use the genome assembly:

• Start IGB (http://www.bioviz.org/igb)
• Select Current Genome tab (right)
• Select Species Sorghum bicolor, Genome Version S_bicolor_Jun_2013 (the latest)

The gene models from Phytozome (re-formatted for IGB) will load automatically from this file:

http://igbquickload.org/quickload/S_bicolor_Jun_2013/S_bicolor_Jun_2013.bed.gz

If you are doing RNA-Seq or similar *Seq experiments, this file - which is in BED-detail format - may be useful. Fields 1 through 12 are the same as ordinary BED. Field 13 contains the gene name and field 14 contains a short, human-readable description of gene function, taken from the "defline" file on Phytozome.

This is useful because you can use the gene field (13) and the sequence, start, and end positions (1, 2, 3) to define genomic coordinates for a gene, which is useful for calculating read coverage over a gene and many other things.

If there are other data sets you'd like us to add, let us know.