Associate the metadata rows with the imported reads. Once the import is completed, you should see the folders and data elements in theNavigation Area as shown in figure 1.įigure 1: The Navigation Area after the tutorial data has been imported.Ĥ. You can alternatively drag-and-drop the zip file into the Navigation Area. Import the data by clicking the ( ) Import button and selecting ( ) Standard Import.Ĭhoose the zip file, leave the import type set to Automatic and save the imported data inyour Navigation Area. Download the following zip file: RNA_Seq_IPA_Dengue.zip.ģ. To download and import the tutorial data:ġ. If you do nothave access to IPA, then please use the third and fourth workflows listed above instead of theones named in the instructions.Īdvanced RNA-Seq analysis with upload to IPA 3 The rest of this tutorial refers to worklows that include uploading results to IPA. RNA-Seq and IPA advanced analysis workflow A reference sequence track for chromosome 17 of the human hg38 genome and corre-sponding gene and mRNA tracks.Ģ.A subset of the reads from the 12 samples described above.The zip file distributed for use with this tutorial contains: To allow the tutorial to be completed in a reasonable amount of time, only a subset ofthe reads that map to chromosome 17 are used here. The data we will analyze in this tutorial was sourced from the PRJNA328591 study, whichincluded 12 mRNA profiles of Dengue virus 2 and mock infected cells at 24 and 36 hours postinfection. You can access the in-built manual by clicking on Help buttons or by selecting the "Help"option under the "Help" menu.Within wizard windows you can use the Reset button to change settings to their defaultvalues.You can request a free trial by clicking onRequest a trial. Installing plugins is described in the CLC Genomics Workbench manual.In addition, you must have access to IPA services. To use workflows that include upload to IPA, you must have the Ingenuity Pathway Analysisplugin installed. In addition,it demonstrates the collaborative power of CLC Genomics Workbench and Ingenuity PathwayAnalysis (IPA) for the analysis and interpretation of RNA-Seq expression data.įor this tutorial, you must be working with CLC Genomics Workbench 20.0 or higher. Advanced RNA-Seq analysis with upload to IPA 2Īdvanced RNA-Seq analysis with upload to IPAThe purpose of this tutorial is to illustrate how workflows can be used to easily run RNA-seqand downstream analyses for multiple samples and multiple groups of samples.
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