MapAl – a tool for RNA-Seq expression profiling

MapAl is a tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. In the post-processing of RNA-Seq reads, it incorporates gene models already at the stage of read alignment, increasing the number of reliably measured known transcripts consistently by 50%. Adding genes identified de novo then allows a reliable assessment of double the total number of transcripts compared to other available pipelines. This substantial improvement is of general relevance: Measurement precision determines the power of any analysis to reliably identify significant signals, such as in screens for differential expression, independent of whether the experimental design incorporates replicates or not.

The software is freely available at

  • Labaj PP, Linggi BE, Wiley HS, Kreil DP. (2012) Improving RNA-Seq Precision with MapAl. Front Genet [Epub ahead of print]. [article]
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