Download analysis files

You can download files for analyses in Ion Reporter™ Software that do not include variants. Examples are Metagenomics analysis results and immune repertoire analyses.

  1. In the Analyses tab, click Overview.
  2. Select an analysis to download, then in the Details section, click Actions > Download Results.

    A notice may appear that states that the request is in progress and that downloaded files are available on the Notifications screen.

  3. To download the file from Ion Reporter™ Software:
    1. Click the Home tab, then click Notifications.
    2. Locate the download notification in the list. You can click Downloads to narrow the list, or refer to the timestamp.
    3. Select the analysis notification that you want to download, then click (Download).
  4. Extract the contents of the directory to access the folders and files.

    A compressed directory named analysis name_All.zip is downloaded. If the Ion Reporter™ Software analysis includes notes, the notes are included in the VCF file contained in this directory.

    Depending on the analysis you selected, the ZIP file may contain the following:

    Folder

    Files

    Plugin outputs

    Contains files related to the plugins used, including: CSV, FASTA, JSON, PNG, and HTML files.

    Results

    Contains files related to the analysis. The folder may contain TXT, FASTA, PDF, CSV, or PNG files.

    QC

    Contains files related to Quality Control metrics that are run for the analysis.

    • <bam_file_basename>.ionstats_alignment.json
    • analysis.bfmask.stats
    • explog_final.txt
    • raw_peak_signal
    • InitLog.txt

    The basecaller_results folder contains the following JSON files:

    • BaseCaller.json
    • datasets_basecaller.json
    • ionstats_tf.json
    • TFStats.json

    Workflow_ Settings

    • Analysis_Settings—Folder that contains a text file of the settings used for the analysis workflow.

    • Module_Configuration_Files—Folder that contains tertiary analysis files, including: INI and PLN (plan) files.

    RNACountsActor-00

    driver_WT_assays_Level.txt

    A tab-delimited text file with 4-columns:
    • column1: Gene name (only driver genes, not partners)
    • column2: The type of assay used to compute the RNA levels (This could be either RNAExonTile or RNAExonVar)
    • column3: A number which is the sum of read-counts from the WT amplicons of the gene (for example, all of the RNAExonTile) divided by the number of WT amplicons for the gene
    • column4: A number which is the proportion of the ratio in column3 from the Total Valid RNA Mapped reads
Related Topics
Parent topic: Analyses