# MMAPPR2 [](https://travis-ci.org/kjohnsen/MMAPPR2) ## Mutation Mapping Analysis Pipeline for Pooled RNA-Seq ### Kyle Johnsen, Nathaniel Jenkins, Jonathon Hill ### Introduction MMAPPR2 maps mutations resulting from pooled RNA-seq data from the F2 cross of forward genetic screens. Its predecessor is described in a paper published in Genome Research (Hill et al. 2013). MMAPPR2 accepts aligned BAM files as well as a reference genome as input, identifies loci of high sequence disparity between the control and mutant RNA sequences, predicts variant effects using Ensembl's Variant Effect Predictor, and outputs a ranked list of candidate mutations. [See vignette for instructions](vignettes/MMAPPR2.Rmd) Publication for the [original MMAPPR](http://genome.cshlp.org/content/23/4/687.full.pdf) ## Installation Notes MMAPPR2 depends on two system tools to function: Samtools and VEP. Both must be installed and in the PATH to be found by the appropriate functions. ### Installing Samtools Instructions to install samtools can be found at https://github.com/samtools/samtools and installation instructions are in the INSTALL file included with samtools. ### Installing VEP You'll need Ensembl VEP, which you can install like this, replacing `my_species` with your species (e.g., `danio_rerio`): git clone https://github.com/Ensembl/ensembl-vep.git cd ensembl-vep perl INSTALL.pl -a ac -s {my_species} This installs the most recent VEP and allows you to create a cache for your desired species, which is what MMAPPR2 expects by default. If you depart from the installation shown here, or if things don't go smoothly, see [Ensembl's instructions](http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer) and make sure any differences are accounted for in the [`VEPFlags`](#configure-vepflags-object) object. *Note:* If you have any trouble installing VEP, using [their Docker image](http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#docker) may save you a lot of hassle. *Note:* We have found that R sometimes has issues finding VEP, especially when perlbrew is used. If you encounter errors at the path to your perl installation to the .Rprofile file. For example: Sys.setenv(PATH=paste("/Path/to/Perlbrew", Sys.getenv("PATH"), sep=":"))