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.
All the GoSTRIPES dependencies are encapsulated in a Singularity container available from our Singularity Hub. Thus, once you know what you are doing, execution could be as simple as
singularity pull https://BrendelGroup.org/SingularityHub/GoSTRIPES.sif
singularity exec GoSTRIPES.sif 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.
Robert A. Policastro, R. Taylor Raborn, Volker P. Brendel and Gabriel E. Zentner (2020) Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq. Genome Research 30, 910--823. https://genome.cshlp.org/content/30/6/910.long.
Original pre-print: at BioRxiv.
Please direct all comments and suggestions to Volker Brendel at Indiana University.