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IRAP - Integrated RNA-Seq Analysis Pipeline

iRAP is a flexible RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of existing tools for mapping reads, quantifying expression and testing for differential expression. Depending upon the application, iRAP can be used to quantify expression at the gene, exon or transcript level.

Please consult the wiki ( for further information.

Problems? Errors?

Errors may occur while running one of the many different pieces of software included in IRAP (e.g., a mapper, a quantification method, etc). If this happens then please report the error directly to the developers of the program.

The authors of IRAP always appreciate receiving suggestions for improvements, and reports of bugs in the pipeline or in the documentation. Please submit them through

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