Workflow Designer Documentation v. 1.14.0
Child pages
  • ChIP-seq Analysis with Cistrome Tools

Versions Compared

Old Version 6

changes.mady.by.user Yuliya Algaer

Saved on

compared with

New Version 7

changes.mady.by.user Yuliya Algaer

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Select Samples tab on the Workflow Designer Palette and double-click on the ChIP-seq analysis with Cistrome tools sample. The following configure wizard appears:

 

HTML
<center>
  <br>
  <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_1.png"/>
  <br> 
</center>
Here you need to choose analysis type and cistrome internal data and click Setup. For treatment tags only analysis type the following workflow appears:

 

HTML
<center>
  <br>
  <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_2.png"/>
  <br> 
</center>

For treatment and control tags analysis type the following workflow appears:

HTML
<center>
  <br>
  <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_3.png"/>
  <br> 
</center>

To run these workflows you need to select input annotations, and output files and directories. Also, if required, you can change parameters of MACS, CEAS, Conservation Plot, SeqPos, Peak2Gene, and Gene Ontology. Use the workflow wizard to guide you through the parameters setup process. The first wizard page appears automatically after the Setup button has been pressed or click Show wizard button on the Workflow Designer toolbar to open it:

HTML
<center>
  <br>
  <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_4.png"/>
  <br> 
</center>

The first wizard page:

...

 

Output type

The directory to store Conduct GO results.

Official gene symbols

Output official gene symbol instead of refseq name.

Distance

Set a number which unit is base. It will get the refGenes in n bases from peak center.

Genome file

Select a genome file (sqlite3 file) to search refGenes.

Title

Title is used to name the output files - so make it meaningful.

Gene Universe

Select a gene universe.

The last wizard page:

HTML
<center>
  <br>
  <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_11.png"/>
  <br> 
</center>

Here you need to input output files and directories for all tools.

MACS output:

 

Output directory

Directory to save MACS output files.

Name

Name string of the experiment. MACS will use this string NAME to create output files like 'NAME_peaks.xls', 'NAME_negative_peaks.xls', 'NAME_peaks.bed', 'NAME_summits.bed', 'NAME_model.r' and so on. So please avoid any confliction between these filenames and your existing files.


CEAS output:

 

Output report file

Path to the report output file. Result for the CEAS analysis.

Output annotations file

Name of tab-delimited output text file, containing a row of annotations for every RefSeq gene. Note that the file is not generated if there is no peak regions input.


Conservation Plot output:

 

Output file

File to store phastcons results (BMP).


SeqPos motif tool output:

 

Output directory

Directory to store seqpos results.

Output file name

Name of the output file which stores new motifs found during a de novo search.

 

Peak2Gene output:

Gene annotations

Location of peak2gene gene annotations data file..

Peak annotations

Location of peak2gene peak annotations data file..

 

Conduct GO output:

 

Output directory

Directory to store Conduct GO results.

Choose these output directories click on the Finish button. Now let’s validate and run the workflow. To validate that the workflow is correct and all parameters are set properly click the Validate workflow button on the Workflow Designer toolbar:

...