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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