There are a growing number of sites performing single cell sequencing experiments, and with them come lots of great questions.

Here are a list of some commonly encountered technical queries, regarding analyses in SeqGeq.


The Good News:

Questions or issues for which we have a quick solution.

Why do I need a free FlowJo Cloud account in order to access SeqGeq?

This new licensing method allows us to offer username / password based authentication – Something we’ve been eager to implement. SeqGeq cannot be authorized using dongles or serial numbers.


Can I analyze my data in SeqGeq?

Yes! SeqGeq is quite versatile with regard to the data it can import. As of now the only commonly used data type it won’t load directly is FCS. Workaround: You can use FlowJo to export FCS data in CSV format in order to get it into SeqGeq.

If you do find other data sets which don’t appear to load into SeqGeq natively, we would very much appreciate examples to get functionality in place which will support all the outlier data types available. (Email:


How do I export data-matrices from SeqGeq?

Select your population(s) of interest, right click on the node, and choose “Export / Concatenate”.


How do I perform differential expression analysis in SeqGeq?

Use the Volcano Plot feature.


How can I check the quality of my data matrix?

Try the Quality Control button. 


I have information from different treatments, subjects, time-points, etc (aka categorical, aka  meta-information parameters) associated with my data-sets. How can I include this information in SeqGeq?

If you have a data matrix whose CellID vector matches a categorical matrix’s CellID vector, SeqGeq can merge the two! Data in the vector should be integer (SeqGeq cannot handle string value annotations correctly, yet). Alternatively you can “roll your own” by entering a vector into your data matrix by hand, in order to incorporate the meta-info. 


What is BaseSpace?

BaseSpace is Illumina’s online environment for genomics analyses.  


Does SeqGeq integrate with BaseSpace?

Yes, integration between SeqGeq and Basespace data is seamless.


Is there a trial version?

Yes, you can sign up for a trial of SeqGeq, following instructions here:


What tools are included with the software?

More features and functions than this one section can describe (see the rest of the pages in this documentation site). To list some of the most popular – Dimensionality reduction (PCA, tSNE and LDA), Downsampling, population filtering, gene filtering, Boolean functions,  differential expression analysis platform, quality control, and a whole host of features implemented by plugin, including: Autogating, KNN clustering, and drop-out event correction.


Do you have example or demo data I can use?

Yes, your instal of SeqGeq will come with demo data files as well as some example gene sets.


The Bad News:

Unfortunately there are some sequencing data analysis features requested, which SeqGeq cannot perform. We consider the following to be a list of high priority functions which we’d like to get implemented in the platform as soon as possible.

Does the delivery of FlowJo Cloud allow for cloud based computation for large data sets in SeqGeq?

Not at this time. For now the FlowJo Cloud is only used for authentication of SeqGeq and FlowJo Envoy.


Can I load data directly from my FlowJo Envoy workflows into SeqGeq?

Not currently – This function is only provided for FlowJo, for now.


Can I export Fold-Change and p-Value information from gene sets created in the volcano plots? (Or other statistics derived from my parameters?)

Not yet.


Can I color map gene view plots in SeqGeq? Setup gene set hierarchies? Perform overlays of genes in the gene view?

Not at this time.


Can I create derived parameters (specific formulas including ratios) from combinations of parameters in SeqGeq, like FlowJo?

No, SeqGeq does not yet have a derived parameter platform implemented.


Can I use SeqGeq to do sequence alignments, single nucleotide polymorphism analysis or genome wide association studies?

No, SeqGeq is a tool for use with gene expression data, i.e. RNAseq, CHiPseq and other quantitative measures. It does not perform other secondary sequencing processes. However many of the results from these other modalities can be readily incorporated into single-cell RNA counts matrix analyses in SeqGeq.


More Help:

For detailed descriptions of the functions and features of SeqGeq, see our other documentation pages on this site.

For training resources check out our webinars and FlowJo University:

To register for a free trial of SeqGeq follow instructions available here:

As always, if you’re having trouble utilizing SeqGeq for any reason, please write to our top notch applications engineers: