scwalls/gostripes

Computational workflows for STRIPE-seq data analyses

GoSTRIPES: Computational workflows for STRIPE-seq data analyses

The GoSTRIPES repository encompasses code and scripts developed in the Brendel and Zentner groups for analyses of STRIPE-seq data. The code conforms to our RAMOSE philosophy: it generates reproducible, accurate, and meaningful results; it is open (source) and designed to be scalable and easy to use.

Quick Start

All the GoSTRIPE dependencies are encapsulated in a Singularity container available from Singularity Hub. Thus, once you know what you are doing, execution could be as simple as

singularity pull --name gostripes.simg shub://BrendelGroup/GoSTRIPES
singularity exec gostripes.simg make

(assuming you have prepared a suitable makefile in your working directory). If you want to just run particular programs pre-installed in the container, take a look at xworkStripes. That script sets up a variable rws ("run with singularity") in your working shell, which allows you to run commands like the following:

$rws fastq-interleave

where fastq-interleave is just one of many programs pre-installed in the container. Please see the HOWTO document for a worked example.

Reference

Robert A. Policastro, R. Taylor Raborn, Volker P. Brendel and Gabriel E. Zentner. (2020) Simple and efficient mapping of transcription start sites with STRIPE-seq. biorXiv. https://doi.org/10.1101/2020.01.16.905182. Submitted.

Contact

Please direct all comments and suggestions to Volker Brendel at Indiana University.