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FindER is intended to overcome sequence depth limitations of many existing tools and provides a common mechanism for identifying enrichment from localized e.
H3K4me3 histone modification, or DNA-protein binding as well as dispersed e. Using these adaptive bins FindER first blacklists alignment artifacts that are typically appear as spurious enriched regions using Input DNA control with an option to use external list of blacklisted regions as well.
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FindER then compares count statistics for the IP al vs. This approach is independent of the unknown relative normalization between IP and control data sets.
After that the proportion of the background like re in the Findsr is evaluate, control data is rescaled and the ificance of the enriched bins is then refined with a False Discovery Rate control process. This al-background separation process can be applied globally or locally. It is free from assumptions about underlying distributions of read density and therefore enables the generation of a normalized al profile after taking into the local al-to-noise ratio [currently, -log p-value ].
This allows for integrative multi-sample analysis for data with comparable al-to-noise ratio, and is especially important in examining the effect of relative al strength on the biology. Additionally various metrics that can be used sngle evaluate a success of the experiment such as al to noise ratio are also computed.
of post-processing options for combining co-located enriched regions and filtering on region size is embedded into the tool. The saturation study using different subsampling strategies is available to the user.
User can also chose to use FindER to rank ificance of enrichment of the IP-al in aingle set of selected regions e. Crucially, FindER is a production grade application.
It is a user friendly tool implemented in Java, and it has been tested on terabyte scale ChIP-Seq data. The corresponding md5sum is: FindER. In order to run FindER you will need to have java 8 installed please see Findwr website for details.
FindER uses samtools If you don't have samtools To see on-line help, please use: java -jar FindER.