MiSeq Reporter performs secondary analysis of data generated on the
MiSeq instrument. The run data can be re-analyzed multiple times
locally by requeueing analysis with MiSeq Reporter. Some common
reasons for requeueing analysis include changing the analysis workflow
or correcting index sequences, sample IDs, or samples names in the
sample sheet. The instructions to edit the sample sheet correctly and
requeue analysis with MiSeq Reporter, either using the web interface
or from the run folder, are provided below. Always make sure that a
sequencing run is not in progress when requeuing analysis with MiSeq Reporter.
How to edit the sample sheet
- Navigate to the MiSeq Analysis run folder on the D drive. For
edit the SampleSheet.csv file, open in it a text editor such as
Notepad. If you use a spreadsheet editor, make sure to save the
sample sheet as a comma separated value (.csv) file. Make sure to
maintain the format of the sample sheet.
- If you create a
new sample sheet, keep a copy of the original sample sheet by
renaming the SampleSheet.csv file to SampleSheet_original.csv. Place
the new sample sheet in the MiSeq Analysis run folder and name it
Requeue analysis of a run using the MiSeq Reporter web interface
- To launch the MiSeq Reporter web interface, open the Internet
Explorer web browser and type http://localhost:8042 in the
- From the MiSeq Reporter web interface, select
the Analyses tab on the top left.
- Locate the run from the
list of available runs in the Analyses tab, click on the checkbox
next to the run name, then select Requeue.
During analysis, a status bar with elapsed time appears on the
Analyses Info tab. If analysis needs to be stopped prior to
completion, select the Stop analysis icon next to the status bar on
the Analysis Info tab.
Requeue without using the MiSeq Reporter web interface
- If the run was sent to BaseSpace Sequence Hub, but has not
been analyzed locally, the run will not be listed in the Analyses
section of the MiSeq Reporter web interface. In these situations,
the analysis must be requeued from the run folder. Once the analysis
is requeued, the run will appear in the MiSeq Reporter web
interface. The following steps outline how to requeue analysis from
the run folder.
- Navigate to the MiSeq Analysis run folder
on the D drive. For example:
- Delete the file called queuedforanalysis.txt (or
QueuedForAnalysis.txt) in the run folder. Deleting this file from
the run folder triggers MiSeq Reporter to start analysis. This file
will reappear (as QueuedForAnalysis.txt) with current date and time
stamp, indicating that MiSeq Reporter has started analyzing the
To view the status of the analysis, open the Internet Explorer web
browser and type http://localhost:8042 in the address
bar to launch the MiSeq Reporter web interface. Select the Analyses
tab on the top left. The run that was just requeued will be at the
bottom of the list. Select the run to see the status bar for the analysis.