CSV - prototyping
Import multiple files at once through bulk upload using a CSV file with extension .csv following the instructions below.
Import using CSV is still under development. The templates and process are subject to change prior to release.

Prototyping and Usability: If you are interested in being a usability tester and providing feedback on the Narrative interface, fill out this google form.

File Formatting

Using a CSV to upload treats the CSV as a directory containing the upload information for multiple files. The CSV must be formatted exactly for the importer to interpret it correctly. Follow the guidelines below once formatting the CSV file.

CSV files require four columns for uploading sequencing data when selecting files:

    1.
    File Type - In the first column, include the file type, which can be SRA Reads, Interleaved FastQ Reads, Non-interleaved FASTQ Reads, GenBank Genome, and GFF Genome.
    2.
    File 1 - This column should be the name of the file including the extension and the path to the file, if it is different from the CSV.
    3.
    File 2 ( as needed) - If a second file is needed, for instance when importing a .gff or non-interleaved reads. Use the same format of file name and extension.
    4.
    Output name - The fourth column is reserved to include the output for the reads object, which will be the object name to use as the input for analysis Apps.

For parameters, three columns need to be filled:

    1.
    Importer Type - In the first column, declare which importer app the parameter applies to.
    2.
    Parameter name - The second column is used to indicate which parameter defined on the row
    3.
    Parameter value - The third column indicates the value of the parameter
Using CSV, files of multiple types can be imported simultaneously, provided the correct formatting is used, e.g.,
File Type or Importer Type
File 1 or Parameter name
File 2 (if required) or Parameter value
Output name
SRA Reads
sam_smith/folder-files/file.sra
sra_reads
SRA Reads Parameters
Sequencing Technology
Illumina or PacBio
SRA Reads Parameters
Single Genome
Yes or No
Interleaved FASTQ
sam_smith/folder-files/file.fastq
fastq_reads
Interleaved FASTQ Reads Parameters
Sequencing Technology
Illumina or PacBio
Interleaved FASTQ Reads Parameters
Single Genome
Yes or No
Non-Interleaved FASTQ
sam_smith/folder-files/forward.fastq
sam_smith/folder-files/reverse.fastq
fastq_F_R
Non-Interleaved FASTQ Parameters
Sequencing Technology
Illumina PacBio
Non-Interleaved FASTQ Parameters
Single Genome
Yes or No
GenBank Genome
sam_smith/folder-files/file.gbk
genome_gbk
GenBank Genome Parameters
Genome Type
Draft Isolate
GenBank Genome Parameters
Source of Genbank File
RefSeq
GFF Genome
sam_smith/folder-files/file.gff
sam_smith/folder-files/file.fasta
genome_gff
GFF Genome Parameters
Genome Type
Draft Isolate
GFF Genome Parameters
Scientific Name
scientific-name
GFF Genome Parameters
Source of GFF File
Other
Media File
sam_smith/folder-files/file.tsv
media_tsv

Download a template and example of a valid import CSV:

Copyable CSV Template - Template.csv
120B
Text
CSV template / example file

Formatting - An example

Say you are importing a pair of non-interleaved FASTQ reads test_R1.fastq and test_R2.fastq as an object called test_reads, you would have a row to select the files and another row for each parameter, e.g.,
Type
File 1 / Parameter
File 2 / Parameter value
Output name
Non-interleaved FASTQ Reads
sam_smith/folder-files/test_R1.fastq
sam_smith/folder-files/test_R2.fastq
test_reads
Non-interleaved FASTQ Reads Parameters
Sequencing Technology
PacBio CLR
Non-interleaved FASTQ Reads Parameters
Single Genome
Yes

Importing a CSV file from your computer

Open the Data Browser slide-out by either clicking the Add Data or Plus buttons in the DATA Panel. Then Drag & Drop the .csv file along with the files to be imported into the drop box.
Drag and Drop a CSV file
Once the file appears in the Staging Area, click the check box next to the file name to select it. Click Import Selected at the bottom right corner.
Select file once it populates the Staging Area
This will open the Import from CSV App. In the App, you can see the contents of the CSV file within the App to verify the file names and import settings. Click "Run" on the upper lefthand corner of the App to import the files from the .csv to the Data Panel.
When the Import from CSV Importer App opens, the file will show within the App
When the Import from CSV Importer App opens, the file will show within the App
Import from CSV will signal that the files have been successfully imported
Once the Importer App has run, the App will signal that the files have been imported.
Import from CSV will signal that the files have been successfully imported
Last modified 28d ago