Trouble Creating new genome file with gene annotations

[Jen Patterson]

I am very new to NGS data analysis and I need to visualize my data alignment on separate strands which I know is possible using this software. My alignment was performed in CLC workbench with tracks.

The issue I am having is that I can load my genome but none of my genes are annotated. For the gene annotations I tried using a gff file (attached) in the gene section of the create genome option.  I also tried adding them as a gene list by copying the list as a bed file format (attached). 

Reference: Bacteriophage T4 

URL: http://www.ncbi.nlm.nih.gov/nuccore/29366675?report=fasta

Any advise would be greatly appreciated. 

[James Robinson]

Hi, the problem is the sequence names in your gff and bed files.  The sequence name in the fasta is

Enterobacteria_phage_T4    (note the underscores)

while the sequence in your annotation files is

Enterobacteria phage T4    (note the spaces)

Try replacing the spaces with underscores.  Generally having spaces in sequence names will cause problems.  For example, bed files are whitespace delimited.

Jim

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<Enterobacteria phage T4 (Gene)_convertedgalaxy.gff><Enterobacteria phage T4 (Gene).bed><Enterobacteria phage T4.fasta>

[Jen Patterson]

Thanks I will give that a try.

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[Jen Patterson]

That worked. Thanks you for your advice. I will have to go back and fix all my data files. 

[V. Chen]

How to have Exome View only? We tried IGV_2.3.97 and couldn't figure out. Is this option available yet? We are trying to view fusion of two genes. Thanks!