ZENBU Cluster with expression: Difference between revisions

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


[[Image:Z_DEX_phase2_soas_overview.png]]
[[Image:Z_DEX_phase2_soas_overview.png|400px]]




⚫
== Display your favorite timecourse expression profile onto Phase2 DPI cluster ==

⚫
Taking the Saos timecourse as an example

⚫
# 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<br>[[Image:Z_Phase2_Track_reconfig.1.png|400px]]
⚫
##** duplicate an existing track whose primary data stream is already the desired experiment pool
⚫
# Reconfigure the track<br>[[Image:Z_Phase2_Track_reconfig.2.png|400px]]
⚫
## In the stream processing section of the reconfigure panel, select '''predefined script'''
⚫
## Search for the processing of you choice<br> keywords : "Phase2", "DPI", "cluster", "collated", "permissive", "robust"<br> be mindful of the genome the script is tailored to.<br>[[Image:Z_Phase2_Track_reconfig.4.png|400px]]
⚫
## (recommended best practice) do not forget to modify the track name and description
## select the visualiztion of choice (ex. "arrow") and set the color to mirror summed expression level <br>[[Image:Z_Phase2_Track_reconfig.5.png|400px]]
## accept the reconfiguration<br>[[Image:Z_Phase2_Track_reconfig.6.png|400px]]


== Finding Phase 2 DPI clusters in DEX or gLyph ==
== Finding Phase 2 DPI clusters in DEX or gLyph ==
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https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Annotation;search=Phase2%20DPI%20cluster
https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Annotation;search=Phase2%20DPI%20cluster


===DEX===
[[Image:Z_DEX_phase2_cluster_data_search.png]]
[[Image:Z_DEX_phase2_cluster_data_search.png|400px]]

===gLyph===
[[Image:Z_gLyph_phase2_cluster_data_search.png]]
[[Image:Z_gLyph_phase2_cluster_data_search.png|400px]]




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


[[Image:Z_DEX_phase2_cluster_processing_search.png]]
[[Image:Z_DEX_phase2_cluster_processing_search.png|400px]]


Selecting the processing script from gLyph
Selecting the processing script from gLyph


[[Image:Z_gLyph_phase2_cluster_processing_search.png]]
[[Image:Z_Phase2_Track_reconfig.3.png|400px]]


⚫
== Display your favorite timecourse expression profile onto Phase2 DPI cluster ==

⚫
Taking the Saos timecourse as an example

⚫
# 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
⚫
# Reconfigure the track<br>[[Image:Z_Phase2_Track_reconfig.1.png]]
⚫
## In the stream processing section of the reconfigure panel, select '''predefined script'''<br>[[Image:Z_Phase2_Track_reconfig.2.png]]
⚫
## Search for the processing of you choice<br> keywords : "Phase2", "DPI", "cluster", "collated", "permissive", "robust"<br> be mindful of the genome the script is tailored to.<br>[[Image:Z_Phase2_Track_reconfig.3.png]]
⚫
## (recommended best practice) do not forget to modify the track name and description
⚫
## accept the reconfiguration<br>[[Image:Z_Phase2_Track_reconfig.4.png]]

Latest revision as of 18:30, 31 October 2012

Saos timecourse example quick overview

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

Z DEX phase2 soas overview.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
          Z Phase2 Track reconfig.1.png
        • duplicate an existing track whose primary data stream is already the desired experiment pool
  2. Reconfigure the track
    Z Phase2 Track reconfig.2.png
    1. In the stream processing section of the reconfigure panel, select predefined script
    2. 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.4.png
    3. (recommended best practice) do not forget to modify the track name and description
    4. select the visualiztion of choice (ex. "arrow") and set the color to mirror summed expression level
      Z Phase2 Track reconfig.5.png
    5. accept the reconfiguration
      Z Phase2 Track reconfig.6.png

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

DEX

Z DEX phase2 cluster data search.png

gLyph

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

Z Phase2 Track reconfig.3.png

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