Push Microbial Reads to KBase

Now that the results have been filtered, you can select microbial reads to transfer to KBase for analysis. Search through the results to identify an organism of interest. Once an organism of interest has been identified:

  • Click the “Download” link under the Resources column

JGI-4

 

  • Read the JGI Data Usage Policy that appears after entering the download area. This statement varies for different organisms, so be sure to read carefully. After agreeing to the policy, click the “Ok” button to continue to the download page.
  • The download page contains the data associated with an organism, organized into folders that reflect the quality of the data and the media on which it is stored within JGI.

Legend

  • Open the folder labeled QC Filtered Raw Data to access the quality controlled FASTQ reads file associated with this organism, or open the Raw Data folder for the unfiltered FASTQ file.
  • Notice that the file name for the QC Filtered Raw Data FASTQ file has a string of text located before the “.fastq.gz” file extension. This string of text refers to a set of filtering parameters used in the quality control processing of the genomic data. To access the legend at right, click the blue box titled “Legend” on the right side of the of download page.
  • Use the checkboxes to the left of the folders and files to select the data to push to KBase. For read data, only those uploaded after July 2012 can currently be pushed to KBase.
  • Select the desired files and click the “Push to KBase” button toward the top of the page. This will open a prompt to sign into KBase with your KBase account credentials.

JGI-5

Push Result

  • After signing into KBase from this prompt, JGI will place the data in a queue for pushing to KBase. Once the data has been successfully pushed, you will receive email with a link to access the data and place it into an existing Narrative.

Email

  • Following this link opens a page within KBase that allows the user to either copy the JGI data into an existing Narrative or launch the Assemble and Annotate Microbial Genome app with this data preloaded. Please see the Assemble and Annotate Microbial Genome tutorial for more information about this app.

Transfer Screen

Alternatively, you can access the data you transferred within the Data Panel:

  • Create a new Narrative or open an existing Narrative.
  • The dataset you transferred can be seen in the Narrative Data Panel under the “Shared With Me” tab. The data you have most recently transferred from JGI will be first on the list. With your JGI data in KBase, you can perform other analyses on it and save your results and commentary to share with collaborators.

JGI-GIF

Completing these steps pushes data from the JGI Genome Portal into a KBase Narrative for further analysis. In the future, users will be able to push more data types from JGI to KBase.

If you have any questions about pushing data to KBase from the JGI Genome Portal, please contact KBase support.