Difference between revisions of "Sole-Search"
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{{Bioinformatics application | {{Bioinformatics application | ||
| − | |sw summary= | + | |sw summary=Determines statistically significant peaks from ChIP experiments |
| − | |bio domain=ChIP- | + | |bio domain=ChIP-seq |
| + | |bio tech=Illumina, | ||
| + | |created at=University of California-Davis, | ||
| + | |maintained=No | ||
| + | |input format=FASTQ, | ||
| + | |language=Java, | ||
}} | }} | ||
== Description == | == Description == | ||
<!-- Describe the application in the space below --> | <!-- Describe the application in the space below --> | ||
| + | We have developed integrated peak-calling and analysis software (Sole-Search) which is available through a user-friendly interface and (i) converts raw data into a format for visualization on a genome browser, (ii) outputs ranked peak locations using a statistically based method that overcomes the significant problem of false positives, (iii) identifies the gene nearest to each peak, (iv) classifies the location of each peak relative to gene structure, (v) provides information such as the number of binding sites per chromosome and per gene and (vi) allows the user to determine overlap between two different experiments. In addition, the program performs an analysis of amplified and deleted regions of the input genome. | ||
| − | + | Part of the Chip-Seq Tool Set | |
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Latest revision as of 10:36, 11 January 2016
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Application data |
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| Biological application domain(s) | ChIP-seq |
|---|---|
| Technology | Illumina |
| Created at | University of California-Davis |
| Maintained? | No |
| Input format(s) | FASTQ |
| Programming language(s) | Java |
Summary: Determines statistically significant peaks from ChIP experiments
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Description
We have developed integrated peak-calling and analysis software (Sole-Search) which is available through a user-friendly interface and (i) converts raw data into a format for visualization on a genome browser, (ii) outputs ranked peak locations using a statistically based method that overcomes the significant problem of false positives, (iii) identifies the gene nearest to each peak, (iv) classifies the location of each peak relative to gene structure, (v) provides information such as the number of binding sites per chromosome and per gene and (vi) allows the user to determine overlap between two different experiments. In addition, the program performs an analysis of amplified and deleted regions of the input genome.
Part of the Chip-Seq Tool Set
Links
References
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