UniqueFeature

Data Stream Processing > Processing Modules > Clustering and collation Modules

Description
The UniqueFeature processing module is clustering style module which combines Features which match a unique or identical criteria. The basic criteria for Features being unique is that they share the same genomic location (chrom/start/end) including the same strand.

Parameters

 *  : if true then features can be on different strands, but still be consider identical as long as they have the same start/end/chrom location.
 *  : if true then features must also have same FeatureSource category to be classified as identical, but do not need to be from exact same FeatureSource.
 *  : if true then features must also have same FeatureSource to be classified as identical.
 *  : defines how expression within matching Experiments between unique features are collated together. Possible values are:
 * sum : sum the expression between multiple primary stream features for each matching experiment into the unique feature
 * min : calculate the minimum expression value between multiple primary stream features for each matching experiment
 * max : calculate the minimum expression value between multiple primary stream features for each matching experiment
 * count : count the number of primary stream features for each matching experiment overlapping the unique feature.
 * mean : calculate the average expression value among primary stream features for each matching experiment overlapping the unique feature

Example
This is a script which incorporates a CalcInterSubfeatures, StreamSubfeatures, UniqueFeature followed by CutoffFilter to generate a set of unique introns which can be displayed with score coloring.

    intron  true  2 </stream_processing> </zenbu_script>

second variation on this script using the internal unique-feature controls of the StreamSubfeatures rather than an external UniqueFeature module <zenbu_script> <stream_processing> <spstream module="CalcInterSubfeatures"/> <spstream module="StreamSubfeatures"> intron</category_filter> true</ignore_strand> <spstream module="CutoffFilter"> 2</min_cutoff> </stream_processing> </zenbu_script>

Example ZENBU view showing this script in use http://fantom.gsc.riken.jp/zenbu/gLyphs/#config=X_wwpjePN9Qi8bqoMur8TB;loc=hg19::chr8:128746973..128755020