Mode

From Array Suite Wiki

Jump to: navigation, search

Contents

Column Mode

ColumnMode.png

Please see the page Column Mode for descriptions.

In NormalizeNgsData

  • When Mode is Count, the normalization is done based on data itself.
  • When Mode is Gene, it is will normalize transcript counts at gene level: get the expression values/counts at gene level by getting sum of their corresponding transcripts; calculate the scaling factor on gene level; apply the same scaling factor to transcript level data.

In External Script (Escript)

In Escript, Mode parameter is telling the program whether the input files are paired or not. Then macros, such as %FilePath% and %FileName%, are assigned accordingly.

/Mode=Single: %FilePath%, %FileName%, %FileNameNoExt%, note file path is full path, and file name has no path but has extension.
/Mode=Paired: %FilePath1%, %FileName1%, %FileNameNoExt1%, %FilePath2%, %FileName2%, %FileNameNoExt2%, %PairPath%, %PairName%. 
/Mode=Multiple:  Generally %Files% is the best macro, unless you need to explicitly specify the delimiter to separate the files, in which case %Files.Space% and %Files.Comma% can be useful.

For example:

Begin RunEScript;
iles
"/home/garyge/Test/_Raw/SRR243575.s.1.fastq
/home/garyge/Test/_Raw/SRR243575.s.2.fastq";
...
.../Mode=Paired
...

Then

%FilePath1%=/home/garyge/Test/_Raw/SRR243575.s.1.fastq
%FilePath2%=/home/garyge/Test/_Raw/SRR243575.s.2.fastq
%FileName1%=SRR243575.s.1.fastq
%FileName2%=SRR243575.s.2.fastq
%FileNameNoExt1%=SRR243575.s.1
%FileNameNoExt2%=SRR243575.s.2
%PairName%=SRR243575.s

Also read:

External Script Integration

Logic to determine paired-end read files and sample name

In Default.template or Sample.template

Mode is for a variety of FieldTypes, including Nextbio and Date based fields.

Options include:

For NextBio:

Type of ontology to be searched, separated by commas, for instance Anatomy, Biosource, Disease, Tissue, etc..

For Date:

The Mode “Auto” will automatically populate it to the current date upon registration of a Sample, SampleSet or publishing of a Project.

Applies to both sample.template and default.template files.

In AnnotateMutation

Specifies whether the table being annotated is a table of mutations or SNP annotation.