Question: Incoperating Annotations (from a GFF file) to a custom built genome
gravatar for Venura
8 months ago by
Sri Lanka, Peradeniya,University of Peradeniya
Venura0 wrote:


I created a custom build using the rubber genome available at NCBI. I would like to incorporate annotations in to the build (already downloaded and added to Galaxy (local server) ). I would be thankful if you can assist me on this regard.


gff ncbi annotation • 312 views
ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson25k • written 8 months ago by Venura0
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Reference annotation can be selected on the tool forms at runtime for most tools that incorporate annotation.

Did you need help finding this option with a specific tool? Let us know which as we can help with usage.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson25k

Hi Jen, Thank you for the quick reply. Let me outline what I did and what I am planing to do;

  1. Upload reference genome (GCA_001654055.1) and corresponding annotations (GFF) from NCBI (already completed)
  2. I already completed assembly (to the above reference genome) of two genomes (one susceptible and one tolerant clone) using BWA- please note this was done outside galaxy.
  3. As a result, I have two BAM files coming from the alignment.
  4. I also did variant calling using SAMtools (again outside galaxy) for the above.
  5. So , I have two VCF files as well.

What I wanted to do is to find CNV among two genomes. So I was planing to upload all files to galaxy and do the analysis and visualize.

I uploaded both reference genome (.fna) and annotations (.gff) . but now I am stuck there trying to figure out how to merge them together and visualize(like you see it in IGV or JBrowse) and also how to proceed there after.

Sorry for the inconvenience. I really appreciate your assistance . Thank you, Venura

ADD REPLYlink written 8 months ago by Venura0

Hi Venura, Thanks for explaining. All of this data can be uploaded to Galaxy and used together. A fasta dataset can be used a custom reference genome with most tools, including Trackster ("Visualizations") - promote it to a custom build and assign that as a database to the other datasets based on it. Hope that helps! Jen

Galaxy tutorials: FAQs for Custom genomes/builds, metadata assignments, and more:

ADD REPLYlink written 8 months ago by Jennifer Hillman Jackson25k
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