Question: visualize tophat output on custom (zerbafish) genome, output not in list
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2.7 years ago by
f.j.vaneeden0 wrote:

I am a beginner so this may be a basic question....I have taken 2 rnaseq datasets from the geo database mapped these to the zebrafish genome using tophat in galaxy, as the zebrafish genome is not available for tophat, I uploaded the ensembl zv9 genome apparently successfully in my history and tophat appeared to run successfully and generated output that seemed ok as far as i can judge. Next I wanted to visualise the data using the built in zebrafish genome using the visualisation tool in galaxy, but in this case my tophat datasets are simply not "listed". I gathered that this was because I mapped to my "custom uploaded zf genome" in tophat. Therefore I used " Add a Custom Build" again, to add exactly the same genome as was used in tophat for mapping. I thought I had now cracked the problem but, when using that custom genome, I -again- did not get my tophat outputs listed in the menu "add data sets" ...does anyone have an idea why this is?? are my datasets too big maybe? do the tophat outputs further manipulation before they can be "seen" as datasets by the visualisation tool?? Are there still plans to add a zf genome to the bult in genomes in tophat? Any help is welcome...

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