Difference between revisions of "MakeStrandless"

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(Created page with "==Description== The '''MakeStrandless''' processing module is designed to apply the TPM (''tag-per-million'') normalization procedure onto e...")
 
(Description)
 
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__NOTOC__
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[[DataProcessing | Data Stream Processing]]
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>
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[[DataProcessing#Processing_modules | Processing Modules]]
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>
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[[DataProcessing#General_manipulation | General manipulation Modules]]
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==Description==
 
==Description==
The '''MakeStrandless''' [[DataProcessing#Processing_modules|processing module]] is designed to apply the TPM (''tag-per-million'') normalization procedure onto expression data. When data is loaded into the ZENBU system from [[BED|BED]] or [[OSCtable|OSCtable]] files, a '''total''' is calculated for every expression Experiment column. This total can be used to transform those expression values into a ''per-million'' normalized form.
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The '''MakeStrandless''' [[DataProcessing#Processing_modules|processing module]] processes [[DataModel#Feature|'''Features''']] on the data stream and removes their strand information to make them strandless. Useful when the data are alignments (which inherently are stranded), but the experimental sample protocol is actually strandless in nature and the strand information present in the alignment is meaningless.
  
 
==Parameters==
 
==Parameters==
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<pre>
 
<pre>
 
<zenbu_script>
 
<zenbu_script>
   <stream_queue>
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   <stream_processing>
<spstream module="MakeStrandless"/>
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<spstream module="MakeStrandless"/>
   </stream_queue>
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 +
<spstream module="TemplateCluster">
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<overlap_mode>height</overlap_mode>
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<expression_mode>sum</expression_mode>
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<overlap_subfeatures>true</overlap_subfeatures>
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<ignore_strand>true</ignore_strand>
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<side_stream>
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<spstream module="FeatureEmitter">
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<fixed_grid>true</fixed_grid>
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<both_strands>false</both_strands>
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</spstream>
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</side_stream>
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</spstream>
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   </stream_processing>
 
</zenbu_script>
 
</zenbu_script>
 
</pre>
 
</pre>

Latest revision as of 17:12, 6 June 2013

Data Stream Processing > Processing Modules > General manipulation Modules

Description

The MakeStrandless processing module processes Features on the data stream and removes their strand information to make them strandless. Useful when the data are alignments (which inherently are stranded), but the experimental sample protocol is actually strandless in nature and the strand information present in the alignment is meaningless.

Parameters

This module has no parameters

Example

Simple script...

<zenbu_script>
   <stream_processing>
		<spstream module="MakeStrandless"/>

		<spstream module="TemplateCluster">
			<overlap_mode>height</overlap_mode>
			<expression_mode>sum</expression_mode>
			<overlap_subfeatures>true</overlap_subfeatures>
			<ignore_strand>true</ignore_strand>
			<side_stream>
				<spstream module="FeatureEmitter">
					<fixed_grid>true</fixed_grid>
					<both_strands>false</both_strands>
				</spstream>
			</side_stream>
		</spstream>
   </stream_processing>
</zenbu_script>