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# FRASER - Find RAre Splicing Events in RNA-seq [![Build](]( [![Version](]( [![Coverage status](]( [![License](]( FRASER is a tool to detect aberrant splicing events in RNA-seq data. The method is described and published in [Nature Communications]( and available through [Bioconductor]( It is also part of the [Detection of RNA Outlier Pipeline (DROP)]( The DROP pipeline is described and published in [Nature Protocols]( The FRASER framework and workflow aims to assist the diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects. For a short tutorial on how to use FRASER on a dataset please use the [vignette]( or our Colab tutorial at: []( The Colab is based on a workshop that we presented at ASHG 2019/2020. Please cite our method paper if you use it in a publication: > Mertes, C., Scheller, I.F., YĆ©pez, V.A. *et al.* Detection of aberrant splicing events in RNA-seq data using FRASER. *Nat Commun* **12**, 529 (2021). ## Installation `FRASER` is an R/Bioconductor software package requiring a running [R 3.6 version or higher]( The recommanded way of installing `FRASER` is to use `Bioconductor`: ``` if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages('BiocManager') BiocManager::install('FRASER') ``` If you use an R version below `4.0.0` you have to install it from source. To this end, we will use `devtools` to install it. For this, you need a working development environment to compile the C++ code (see for details: [Windows]( or [MacOS X]( ``` if (!requireNamespace("devtools", quietly=TRUE)) install.packages('devtools') # latest development version devtools::install_github('gagneurlab/FRASER', dependencies=TRUE) # or a specific version of FRASER (search for tags on github) devtools::install_github('gagneurlab/FRASER', ref='1.1.3', dependencies=TRUE) ``` If you have dependency issues while installing any package, please have a look at the Troubleshooting section or submit an issue on [GitHub]( ### Toubleshooting #### Error in UseMethod("filter_") When using FRASER with R3.6 one might observe the following error: ``` fds <- annotateRanges(fds) # Error in UseMethod("filter_") : # no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')" ``` To overcome this error one needs to upgrade BiocFileCache. ``` BiocManager::install("Bioconductor/BiocFileCache", ask=FALSE, update=FALSE) ``` #### Missing libraries while compiling R packages On some Linux distributions we need the developer libraries for compiling the R packages. To install those packages, please run as administrator: For Ubuntu or debian based systems: ``` sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev zlib1g-dev libmysqld-dev ``` For centOS or RHEL based systems: ``` sudo yum install R-devel zlib-devel openssl-devel libcurl-devel libxml2-devel mariadb-devel ```