However, the fasta of the full genome of the species in many pieces (32). I have tried Getdata/Collection/Paste-Fetch data. There I pasted all the 32 URLs(links) to the files.
After, there was an option to build a list. I created the list. Now I have no idea what to do. How I can reconstruct the full file or one file with all sequences…I mean how I will get the full genome of the species?
The links are on the genome assembly page at NCBI.
The compression for .gz data is supported by the Upload tool. However, some data will uncompress upon upload to be available to tools. Use “autodectect” with the Upload tool to prevent problems/mismatched datatypes.
Yes, fna is a sub-version of fasta data. It designates a nucleotide fasta sequence. Galaxy will assign the datatype fasta. The reference annotation is named with gff (but is actually in gff3 format) and Galaxy will assign the datatype gff3. The README docs at this level and higher up explain the content at this site.
@jennaj, I am using maize RNA seq in galaxy for analysis, but there is no inbuilt maize reference genome. I cant download it from NCBI due to its huge size. Can Galaxy team upload Zea mayz reference genome to galaxy
The reference genome mm10 is already installed at all of the usegalaxy.* servers, and is indexed for most tools.
Some tools require that the input to the tool has the datatype assigned. This can filter options on the tool form. In your case, this would be assigning the metadata for the datatype mm10 to the input. Try doing that and see if it resolves the problem. How-to: Metadata
If you are running your own Galaxy server or using some private Galaxy server, genomes are not added or indexed for tools by default. The genome will usually show up in the list of “databases” on the Upload or Edit attribute forms, but those are just references. The actual data need to be added, and that can include genomes that are not already in the list of databases (when you add the data, it will be added to that list). These prior Q&A topics explain how-to, along with some troubleshooting help. You need to be the administrator of the server to do this. If you are not the administrator, ask them to do it and maybe point them to the help.
