ZENBU Cluster with expression: Difference between revisions

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# select the CTSS data to be pooled
# select the CTSS data to be pooled
#*from DEX (when creating a novel view)
##*from DEX (when creating a novel view)
#*from gLyph (when adding the track to an preexisting view)
##*from gLyph (when adding the track to an preexisting view)
# search for the experiment to be pooled
##** search for the experiment to be pooled
#* duplicate an existing track whose primary data stream is already the desired experiment pool
##** duplicate an existing track whose primary data stream is already the desired experiment pool

# Reconfigure the track
# Reconfigure the track
<br>[[Image:Z_Phase2_Track_reconfig.1.png]]
<br>[[Image:Z_Phase2_Track_reconfig.1.png]]

Revision as of 17:48, 31 October 2012

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Finding Phase 2 DPI clusters in DEX or gLyph

keywords : "Phase2" "DPI" "cluster"

https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Annotation;search=Phase2%20DPI%20cluster

Z DEX phase2 cluster data search.png

Z gLyph phase2 cluster data search.png


Finding the proper processing script

keywords : "Phase2" "DPI" "cluster" "collated"

Overview of available canned processing scripts : https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Scripts;search=Phase2%20DPI%20collated

Z DEX phase2 cluster processing search.png

Selecting the processing script from gLyph

File:Z gLyph phase2 cluster processing search.png


Display your favorite timecourse expression profile onto Phase2 DPI cluster

Taking the Saos timecourse as an example

  1. select the CTSS data to be pooled
      • from DEX (when creating a novel view)
      • from gLyph (when adding the track to an preexisting view)
        • search for the experiment to be pooled
        • duplicate an existing track whose primary data stream is already the desired experiment pool
  2. Reconfigure the track


Z Phase2 Track reconfig.1.png

    1. In the stream processing section of the reconfigure panel, select predefined script


Z Phase2 Track reconfig.2.png

    1. Search for the processing of you choice


keywords : "Phase2", "DPI", "cluster", "collated", "permissive", "robust"
be mindful of the genome the script is tailored to.
Z Phase2 Track reconfig.3.png

    1. (recommended best practice) do not forget to modify the track name and description
    2. accept the reconfiguration


Z Phase2 Track reconfig.4.png

Saos timecourse example

https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=ndJNXLSZEdNkcx4tzUkdY;loc=hg19::chr19:36600502..36617366

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