@@ -8,7 +8,7 @@ The method is actually a combination of scripts that depend on each other. To ea
Depending on how deep your original material was sequenced (i.e. how big your input files are in terms of the memory usage), your computer might require **50 GB of available memory (RAM)** to process these files. [Snakemake](https://snakemake.readthedocs.io/en/stable/) is used to facilitate the automated execution of all analysis steps. The easiest way to make use of the pipeline is to set up a python3 and a python2 virtual environment and run the pipeline in the python3 environment. Instructions on how to install the virtual environments for the analysis are given in the README of the main directory of this repository.
### snakemake
Snakemake is a workflow management system that helps to create and execute data processing pipelines. It requires python3 and can be most easily installed via the bioconda package of the python anaconda distribution. You're setup right after the following steps:
[Snakemake](https://snakemake.readthedocs.io/en/stable/) is a workflow management system that helps to create and execute data processing pipelines. It is already part of the virtual environment which was introduced in the introduction README.
### activate the python 3 environment
Please see the README file one level up. There you can find information how to install miniconda and how to create a python3 environment that is used now to run the pipeline.
@@ -9,11 +9,8 @@ git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_public/PAQR_KAPAC.git pat
cd path/to/workdir
```
## Use case of the pipeline
Below, you will find a tutorial that guides you through the usage of PAQR and KAPAC based on the RNA-seq data set to study the knock-down of HNRNPC. The results for this data set are also discussed in the paper.
### snakemake
[Snakemake]{https://snakemake.readthedocs.io/en/stable/} is a workflow management system that helps to create and execute data processing pipelines. Here, it is used to run the PAQR pipeline. It requires python3 and can be installed smoothly via the bioconda package of the python anaconda distribution (shown below).
## Prepare the virtual environment
The execution of PAQR and KAPAC depends on specific software (like python, including several packages, or R). With the installation and activation of the virtual environment as it is shown below, you can ensure that both tools run properly.
