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Gene annotations table | Path to gene annotation table (e.g. a refGene table in sqlite3 db format. |
Span size | Span from TSS and TTS in the gene-centered annotation (base pairs). ChIP regions within this range from TSS and TTS are considered when calculating the coverage rates in promoter and downstream. |
Wiggle profiling resolution | Wiggle profiling resolution. WARNING: Value smaller than the wig interval (resolution) may cause aliasing error. |
Promoter/downstream interval | Promoter/downstream intervals for ChIP region annotation are three values or a single value can be given. If a single value is given, it will be segmented into three equal fractions (e.g. 3000 is equivalent to 1000,2000,3000). |
BiPromoter ranges | Bidirectional-promoter sizes for ChIP region annotation. It's two values or a single value can be given. If a single value is given, it will be segmented into two equal fractions (e.g. 5000 is equivalent to 2500,5000). |
Relative distance | Relative distance to TSS/TTS in WIGGLE file profiling. |
Gene group files | Gene groups of particular interest in wig profiling. Each gene group file must have gene names in the 1st column. The file names are separated by commas. |
Gene group names | Set this parameter empty for using default values. The names of the gene groups from "Gene group files" parameter. These names appear in the legends of the wig profiling plots. Values range: comma-separated list of strings. Default value: 'Group 1, Group 2,...Group n'. |
Click Next. The next page allows you to configure Conservation Plot parameters:
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<center> <br> <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_7.png"/> <br> </center> |
The following parameters are available:
Title | Title of the figure. |
Label | Label of data in the figure. |
Assembly version | The directory to store phastcons scores. |
Window width | Window width centered at middle of regions. |
Height | Height of plot. |
Width | Width of plot. |
Optionally choose these parameters and click Next. The next page contains SeqPos motif parameters:
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<center> <br> <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_8.png"/> <br> </center> |
The following parameters are available:
Genome assembly version | UCSC database version. |
De novo motifs | Run de novo motif search. |
Motif database | Known motif collections. |
Region width | Width of the region to be scanned for motifs; depends on a resolution of assay. |
Pvalue cutoff | Pvalue cutoff for the motif significance. |
Optionally, modify these parameters and click Next. The next page contain Peak2Gene and Gene Ontology parameters:
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<center> <br> <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_9.png"/> <br> </center> |
You can configure the following parameters:
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:
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<center> <br> <img src="/wiki/download/attachments/3244619/ChIP-seq analysis with Cistrome tools_10.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.
Note that default button reverts all parameters to default settings.
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:
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