MiSeq Reporter Common Questions

What browsers are supported for MiSeq Reporter?

MiSeq Reporter can be viewed with the following web browsers: Firefox 13.0.1+, IE 11+, and Safari 5.1.7+.

Silverlight support has been discontinued for these browsers (Firefox 13.0.1+ and Safari 5.1.7+), so without Internet Explorer, an upgrade to a control software with LRM is required.

Silverlight can be downloaded from here: https://www.filehorse.com/download-silverlight-64/download/)

How do I know that MiSeq Reporter has completed its analysis?

When MiSeq Reporter analysis is finished, a checkmark appears in the State column of the Analyses tab and the CompletedJobInfo.xml file is written to the root level of the analysis folder.

Does the Library QC workflow in MiSeq Reporter perform alignment?

Yes, alignment is performed in the Library QC workflow; however, it is performed using a faster and less sensitive setting, which provides a much faster turnaround time. Variant calling is not employed for this workflow.

How do I access MiSeq Reporter?

The MiSeq Reporter interface can only be viewed through a web browser. To view the MiSeq Reporter interface during analysis, open any web browser on a computer with access to the same network as the MiSeq system. Connect to the HTTP service on port 8042 using one of the following methods:

MiSeq Reporter indicates that I have a sample numbered 0. What is sample 0?

Sample 0 is not designated in the samplesheet. Reads that were not successfully assigned to a sample are written to a FASTQ file for sample number 0, and excluded from downstream analysis.

Can secondary analysis run on MiSeq while a run is in progress?

If a new sequencing run is started on the MiSeq before secondary analysis of a previous run is complete, secondary analysis will be stopped automatically. MiSeq computing resources are dedicated to either sequencing or analysis, and the system is designed in such a way that a sequencing command overrides an analysis command. Secondary analysis can later be requeued from the MiSeq Reporter Analyses tab.

How do I requeue a run for analysis in MiSeq Reporter?

MiSeq Reporter needs to have access to the repository, which is the location of the folder containing data for analysis. You can set this location in the settings window on the MiSeq Reporter main screen. When MiSeq Reporter has access to the repository, your runs appear in the Analyses tab in MiSeq Reporter. Select the Requeue checkbox next to the run you want to analyze, and then click Requeue to start analysis.

How long does it take for MiSeq secondary analysis to complete?

For a 2 x 250 bp run, analysis takes about 3 hours. This timing is dependent on running the latest PC RAM configuration on the MiSeq. This also depends on the genome size for resequencing. If analysis is taking longer than two hours, consider mapping to a more appropriate reference for your sample, or perform analysis offline by installing MiSeq Reporter on another computer.

If an alignment is performed against the whole genome, then the analysis time will be significantly longer than two hours. Also, bioinformatics analysis for metagenomics may take as long as 12 hours.

Can secondary analysis by MiSeq Reporter be delayed after a sequencing run completes?

No, secondary analysis cannot be delayed automatically. Secondary analysis will automatically stop if you begin the run setup steps for a subsequent sequencing run on the MiSeq.

Is the version of MiSeq Reporter software used for analysis recorded in the run folder?

The MiSeq Reporter software version can be found in the following files located at the root level of the run folder: the log file AnalysisLog.txt, the CompletedJobInfo.xml file, and the workflow-specific results file (e.g. ResequencingRunStatistics.xml).

In what format does MiSeq Reporter output aligned data?

MiSeq Reporter outputs aligned data in the BAM file format.

Does MiSeq Reporter recognize \.fasta or \.fa?

Yes, MiSeq Reporter recognizes both extensions.

What genomes and databases are used for alignment and variant detection?

The MiSeq comes with pre-installed databases, which include miRbase, dbSNP, and refGene. Also included are eight genomes: arabidopsis, cow, DH10b, hg19, mouse, rat, yeast, and s. aureus. You can upload your own references in fasta format (\.fasta or \.fa).

Can the MiSeq generate FASTQ files?

FASTQ files are generated during secondary analysis by MiSeq Reporter for most analysis workflows. To generate only FASTQ files, specify the GenerateFASTQ workflow in the sample sheet, which generates FASTQ files and then exits secondary analysis.

For any feedback or questions regarding this article (Illumina Knowledge Article #2240), contact Illumina Technical Support [e-mail].