Questions or issues\u00a0for which we have a quick solution.<\/em><\/p>\n Why do I need a free FlowJo Cloud account in order to access SeqGeq?<\/strong><\/p>\n This new licensing method allows us to offer username \/ password based authentication – Something we\u2019ve been eager to implement. SeqGeq cannot be authorized using dongles or serial numbers.<\/span><\/p>\n \u00a0<\/p>\n Can I analyze my data in SeqGeq?<\/strong><\/p>\n Yes! SeqGeq is quite versatile with regard to the data it can import<\/a>. As of now the only commonly used data type it won\u2019t load directly is FCS. Workaround<\/strong>: You can use FlowJo to export FCS data in CSV format in order to get it into SeqGeq.<\/span><\/p>\n If you do find other data sets which don\u2019t 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: <\/span>seqgeq@flowjo.com<\/span><\/a>)<\/span><\/p>\n \u00a0<\/p>\n How do I export data-matrices from SeqGeq?<\/strong><\/p>\n Select your population(s) of interest, right click on the node, and choose \u201cExport \/ Concatenate\u201d. <\/span><\/p>\n \u00a0<\/p>\n How do I perform differential expression analysis in SeqGeq?<\/strong><\/p>\n Use the Volcano Plot<\/a> feature.<\/span><\/p>\n \u00a0<\/p>\n How can I check the quality of my data matrix?<\/strong><\/p>\n Try the Quality Control<\/a> button.\u00a0<\/span><\/p>\n \u00a0<\/p>\n I have information from different treatments, subjects, time-points, etc (aka categorical, aka \u00a0meta-information parameters) associated with my data-sets. How can I include this information in SeqGeq?<\/strong><\/p>\n If you have a data matrix whose CellID vector matches a categorical matrix\u2019s 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 \u201croll your own\u201d by entering a vector into your data matrix by hand, in order to incorporate the meta-info.\u00a0<\/span><\/p>\n \u00a0<\/p>\n What is BaseSpace?<\/strong><\/p>\n BaseSpace is Illumina\u2019s online environment for genomics analyses. \u00a0<\/span><\/p>\n \u00a0<\/p>\n Does SeqGeq integrate with BaseSpace?<\/strong><\/p>\n Yes, integration between SeqGeq and Basespace data is seamless. <\/span><\/p>\n \u00a0<\/p>\n Is there a trial version?<\/strong><\/p>\n Yes, you can sign up for a trial of SeqGeq, following instructions here:<\/span><\/p>\n www.flowjo.com\/solutions\/seqgeq\/free-trial<\/span><\/a><\/p>\n \u00a0<\/p>\n What tools are included with the software?<\/strong><\/p>\n 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, \u00a0differential expression analysis platform, quality control, and a whole host of features implemented by plugin, including: Autogating, KNN clustering, and drop-out event correction.<\/span><\/p>\n \u00a0<\/p>\n Do you have example or demo data I can use?<\/strong><\/p>\n Yes, your instal of SeqGeq will come with demo data files as well as some example gene sets.<\/span><\/p>\n \u00a0<\/p>\n Unfortunately there are some sequencing data analysis features requested, which SeqGeq cannot perform.\u00a0We consider the following to be a list of high priority functions which we’d like to get implemented in the\u00a0platform as soon as possible.<\/em><\/p>\n Does the delivery of FlowJo Cloud allow for cloud based computation for large data sets in SeqGeq?<\/strong><\/p>\n Not at this time. For now the FlowJo Cloud is only used for authentication of SeqGeq and FlowJo Envoy.<\/span><\/p>\n \u00a0<\/p>\n Can I load data directly from my FlowJo Envoy workflows into SeqGeq?<\/strong><\/p>\n Not currently – This function is only provided for FlowJo, for now.<\/span><\/p>\n \u00a0<\/p>\n Can I export Fold-Change and p-Value information from gene sets created in the volcano plots? (Or other statistics derived from my parameters?)<\/strong><\/p>\n Not yet.<\/span><\/p>\n \u00a0<\/p>\n Can I color map gene view plots in SeqGeq? Setup gene set hierarchies? Perform overlays of genes in the gene view?<\/strong><\/p>\n Not\u00a0at this time.<\/span><\/p>\n \u00a0<\/p>\n Can I create derived parameters (specific formulas including ratios) from combinations of parameters in SeqGeq, like FlowJo?<\/strong><\/p>\n No, SeqGeq does not yet have a derived parameter platform implemented.<\/span><\/p>\n \u00a0<\/p>\n Can I use SeqGeq to do sequence alignments, single nucleotide polymorphism analysis or genome wide association studies?<\/strong><\/p>\n 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.<\/span><\/p>\n \u00a0<\/p>\n For detailed descriptions of the functions and features of SeqGeq, see our other documentation pages on this site.<\/span><\/p>\n For training resources check out our webinars and FlowJo University:<\/span><\/p>\n www.flowjo.com\/learn\/webinars<\/span><\/a><\/p>\n www.flowjo.com\/learn\/flowjo-university\/seqgeq<\/span><\/a><\/p>\n To register for a free trial of SeqGeq follow instructions available here:<\/span><\/p>\n www.flowjo.com\/solutions\/seqgeq\/free-trial<\/span><\/a><\/p>\n As always, if you\u2019re having trouble utilizing SeqGeq for any reason, please write to our top notch applications engineers: seqgeq@flowjo.com<\/a><\/span><\/p>\n \u00a0<\/p>\nThe Bad News:<\/span><\/h2>\n
More Help:<\/span><\/h2>\n
![\"\"](\"https:\/\/docs.flowjo.com\/wp-content\/uploads\/2020\/08\/seqgeq-1.png\")
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