# GoSTRIPES


# GoSTRIPES: Computational workflows for STRIPE-seq data analyses

The GoSTRIPES repository encompasses code and scripts developed in the
[Brendel](http://brendelgroup.org/) and [Zentner](http://zentnerlab.bio.indiana.edu/)
groups for analyses of STRIPE-seq data.
The code conforms to our [RAMOSE](https://brendelgroup.github.io/)
philosophy: it generates __reproducible__, __accurate__, and __meaningful__
results; it is __open__ (source) and designed to be __scalable__ and
__easy__ to use.


## Quick Start [![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/1990)

All the GoSTRIPE dependencies are encapsulated in a
[Singularity](https://www.sylabs.io/docs/) container available from
[Singularity Hub](https://singularity-hub.org/).
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](./bin/xworkStripes).
That script sets up a variable _rws_ ("run with singularity") in your working
shell, which allows you to run commands like the following:

```console
$rws fastq-interleave
```

where _fastq-interleave_ is just one of many programs pre-installed in the
container. Please see the [HOWTO](./HOWTO.md) 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](<mailto:vbrendel@indiana.edu>)
at [Indiana University](http://brendelgroup.org/).

# To activate

Run this:

```console
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!):

```console
$rws <PROGRAM>
```

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

```console
$rws make
```

--

Location:

```console
$ 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>