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

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:

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$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.

To activate

Run this:

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bash
source /local/cluster/singularity-images/gostripes/activate.sh

Then, you can access the programs in the GoSTRIPES singularity image using the syntax (don’t forget the $rws part!):

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$rws <PROGRAM>

The authors of GoSTRIPES suggest using a makefile, in which case you would run

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$rws make

–

Location:

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$ ls /local/cluster/singularity-images/gostripes/STRIPES/gostripes.simg
/local/cluster/singularity-images/gostripes/STRIPES/gostripes.simg

software ref: https://github.com/BrendelGroup/GoSTRIPES
research ref: http://dx.doi.org/10.1101/gr.261545.120