The Basic RNA-Seq Workflow process runs a basic workflow for RNA-Seq data, including options for quality control and ANOVA.
Note: This process is considered experimental.
Two data sets are required:
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An Input Data Set that contains all of the numeric data to be analyzed. The sam_mus_gse18905_chr1_6s.sas7bdat data set serves as an example, and is partially shown below. It has 12 columns and 3421 rows. Note that this is a tall data set.
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An Experimental Design Data Set (EDDS). This data set tells how the experiment was performed, providing information about the columns in the input data set. The edf_mus_gse18905_chr1_6s.sas7bdat EDDS serves as an example, and is shown below. Note that one column in the EDDS must be named ColumnName and the values contained in this column must exactly match the column names in the input data set.
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Two files are optional:
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An Annotation Data Set. This data set contains other annotation information for each of the markers.
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A tracks settings file. This file is a SAS settings (.sas) file, generated from a text file using the Track Gene Text process. This settings file defines a track for a set of genes and is used to embellish the p-value plot with depictions of genes.
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For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.
When you click , the Basic RNA-Seq Workflow process begins by opening the Workflow Builder. The Workflow Builder builds a settings file for each process containing the information from the data sets and parameters specified in the Basic RNA-Seq Workflow dialog. Once the setting files are generated and saved, the individual processes in the workflow are sequentially opened, populated, and run. The results of the processes are saved in the specified output folder. Finally, a JMP journal, providing links to the workflow dialog and the results of each process, is generated. The Journal is shown below.
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Click .
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The Workflow Builder dialog shows the settings for each of the processes in the workflow. You can select and edit individual settings to adjust your analysis.
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Click under any of the processes shown in the journal to view the output for those processes. For your convenience, links to default Basic RNA-Seq Workflow processes are given below.
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