You can download files for analyses in Ion Reporter™ Software that do not include variants.
Examples are Metagenomics analysis results and immune repertoire analyses.
In the Analyses tab, click Overview.
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.
To download the file from Ion Reporter™ Software:
Click the Home tab, then click Notifications.
Locate the download notification in the list. You can click Downloads to narrow the list, or refer to the timestamp.
Select the analysis notification that you want to download, then click (Download).
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
(Download)