The user’s manual is a practical reference for analysing sequins with Anaquin. Where possible, we have described the use and analysis of sequins in the context of real-life experimental scenarios. The manual also provides step-by-step tutorials, example outputs, usage options and other useful information.
USAGE & OPTIONS
COMMAND LINE & R TOOL OPTIONS
Anaquin includes a range of tools to help analyse sequins in a next-generation sequencing library. Please find below a list of the available tools in both command line and R programming environments, with a brief description of applications, optional arguments, example output results and other useful information.
|RnaAlign||Measure spliced read alignments from sequins on the in silico chromosome.|
|RnaAssembly||Compares assembled transcript models to sequin annotations in the in silico chromosome.|
|RnaExpression||Quantitative analysis of sequin expression.|
|RnaFoldChange||Assess fold-changes in sequin expression between multiple samples.|
|RnaSubsample||Calibrate sequence coverage of sequins across multiple replicates.|
|AnaquinData||Create an Anaquin dataset. The resulting R-object is required for every Anaquin analysis.|
|PlotLinear||Plot linear model between measured and observed abundance of sequins.|
|PlotLogistic||Plot logistic model of assembly sensitivity against measured abundance for sequins.|
|PlotROC||Plot a receiver operating characteristic (ROC) curve that models true positive rate to false positive rate detection.|
|PlotLODR||Create a Limit-of-Detection Ratio (LODR) plot between measured abundance and confidence (p-value)|
Download the latest version (beta v1.1) of the Anaquin software toolkit, and be sure to update your version regularly to benefit from the latest bug fixes and improvements. Please note that this is a beta release and Anaquin is under active development, and you may be occasionally confronted with bugs we have not yet caught. If this happens to you, please send an email including the command line and error message (if required, we may request some sample data) to email@example.com or open a ticket issue on our GitHub repository – github.com/student-t/Anaquin
COMPILE FROM SOURCE
Anaquin is C++ 0x11 software. To build the software from source, you will need the following dependencies: (1) Eigen (http://eigen.tuxfamily.org) (2) Catch (https://github.com/philsquared/Catch) (3) KLib (https://github.com/attractivechaos/klib) (4) Boost (http://www.boost.org/users/download).
Once the dependencies are installed, run make to build the software. The code requires a C++ 0x11 compiler. We have tested the compilation with g++ and xCode, however, other compilers might also work (Windows is not currently supported). To test your installation, run version check.
$ anaquin –v
INSTALL R PACKAGE
To install Anaquin for the Bioconductor, follow the instructions at https://bioconductor.org/packages/devel/bioc/html/Anaquin.html.