Question: Do I Need To Specify The File Format When I Upload Datasets Using Ftp Method?
gravatar for Du, Jianguang
5.7 years ago by
Du, Jianguang110
Du, Jianguang110 wrote:
Hi Everyone, When I upload my datasets onto my history via FTP method (using FileZilla), do I need to specify the file format under "File Format" of "Upload File from your computer"? I noticed that the screencast of how to upload datasets via FTP just leaves the "File Format" as "Auto-detect". However, I also noticed this sentence in the help for Auto-detect: "the system will attempt to detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular, Wiggle, Bed and Interval (Bed with headers) formats". Do I need to specify the format of my datasets if the format of my datasets is not listed in the sentence above? Thanks. Jianguang
gff • 1.1k views
ADD COMMENTlink modified 5.7 years ago by Jennifer Hillman Jackson25k • written 5.7 years ago by Du, Jianguang110
gravatar for Jennifer Hillman Jackson
5.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Jianguang, Setting the type during loading from the FTP area into a history as a dataset is optional. Through experience, I believe that this helps to speed up the process, but this is purely anecdotal. For datasets that have been imported, but have not had format auto-detected, or the format detected was incorrect or not specific enough (e.g. "fastq" when you want "fastqsanger"), just edit the dataset's attributes. Click on the pencil icon in the upper right corner of any dataset, click on the dataset tab in the form that comes up in the middle panel, pick the type from the menu, and save. This can be done with any dataset, at any point. After running certain tools, reassignment of datatype or other metadata (column assignments, found on the first tab of the same "Edit Attributes" form above) is needed - often the tool will note if this is the case. Galaxy has some logic that will prevent the misalignment of obviously incorrect metadata - including widely inappropriate datatypes. But tuning the type to be specific and correct between a group of common format datatypes (for example: a group like "tabular, bed, interval") would be for you to ensure. Setting "database" is also optional and can be performed during or after loading, or at any other time, by clicking through the pencil icon on Edit Attributes form (first tab). In most cases - skip converting spaces to tabs - unless you really are working with a strict tabular dataset and are certain that no fields contain internal whitespace (including informative/metadata headers). Hopefully this helps, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training
ADD COMMENTlink written 5.7 years ago by Jennifer Hillman Jackson25k
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