Question: QUAST Operon Annotations Doubt
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gravatar for y.serranomatos
7 months ago by
y.serranomatos0 wrote:

I am trying to see the quality of my assembly in Quast. I wan to do it with a reference genome and I have to put the annotations genes and operons. I found the first two in ncbi, but cannot find a source where the operon annotations file is accepted by the tool. Can I get a solution to this problem? It seems only to accept .gff files.

gff3 gtf annotations operon quast • 199 views
ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 7 months ago by y.serranomatos0
0
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The option on the form is directly under that for selecting a gene/transcript annotation dataset. Make sure you are using the latest tool version Quast Genome assembly Quality (Galaxy Version 4.6.3) even though the other version (4.1.1) is still available.

From the form's help text. GFF version 2 is labeled with the gtf datatype (no header). GFF version 3 is labeled with the gff3 datatype (and has an intact header). Tabular data is labeled with the datatype tabular.

Inputs and Outputs

Input: The tool accepts assemblies and references in FASTA format. The tool accepts annotation and operon files in:

  • GFF, versions 2 and 3 (note: feature/type field should be either "gene" or "operon")

  • the format used by NCBI for genes ("Summary (text)")

  • four tab-separated columns: sequence name, gene/operon id, start position, end position

FAQs at https://galaxyproject.org/support/#getting-inputs-right

  • Common datatypes explained
  • The tool I'm using does not recognize any input datasets. Why?
  • How do I find, adjust, and/or correct metadata?

These are the tools as installed at Galaxy Main https://usegalaxy.org from the ToolShed. If working somewhere else, with a different tool wrapper/version, and are having problems with the tool accepting inputs (after correctly assigning the datatype) you could request that the administrators of the instance upgrade the tool to the latest ToolShed version or check for other issues.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson25k
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