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.
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
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
- 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