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SplitSeek | Global and unbiased detection of splice junctions from RNA-seq data

Identifies splice junctions. SplitSeek allows de novo prediction of splice junctions in short-read RNA-seq data. The software consists of two programs that are executed sequentially. It can detect novel splice events and be used as a way to extend known gene models. The results can be directly uploaded to the UCSC genome browser and used as input to the BEDTools software suite, which enables user to visualize and analyze the predicted events in a genomic context.

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SplitSeek classification

SplitSeek specifications

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Command line interface
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GNU General Public License version 2.0
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SplitSeek distribution


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SplitSeek support


  • Adam Ameur <>


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Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, Uppsala, Sweden

Funding source(s)

Supported by the Swedish Natural Sciences Research Council.

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