A libray for processing sequencing data for SAturated Transposon Analysis in Yeast (SATAY)
Project description
SATAY and Transposonmapper
This workflow is created for processing sequencing data for SAturated Transposon Analysis in Yeast (SATAY) for Saccharomyces Cerevisiae. It performs the steps from raw sequencing data until the transposon mapping that outputs files containing all insertion sites combined with the number of reads.
For more information regarding SATAY, see the satay user website created by the Kornmann-lab. For more extensive documentation, see our JupyterBook.
The workflow requires input sequencing data in fastq format. It can perform the following tasks:
sequence trimming
quality checking raw and trimmed fastq files
sequence alignment with reference genome (S288C Cerevisiae genome)
quality checking bam files, indexing and sorting
transposon mapping
The output files indicate the location of transposon insertions and the number of reads at those locations. This is presented in both .bed and .wig format. Also a list of genes is generated where the number and distribution of insertions and reads is presented per (essential) gene.
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Documentation for users
PyPI package
For users that only require post processing analysis of the data (the bam file was already analyzed), do use the default installation. For example pysam won’t be installed, hence Linux is not required.
pip install transposonmapper
For users that require the whole processing pipeline, do use:
pip install transposonmapper[linux]
For more extensive documentation, see our JupyterBook.
SATAY pipeline
We provide two methods to run the SATAY pipeline, either with a Docker container (recommended) or a Linux system. The workflow relies on the following libraries:
FASTQC v0.11.9 or later
BBMap v38.87 or later
Trimmomatic v0.39 or later
BWA v0.7.17 or later
SAMTools v1.10 or later
BCFTools v1.10.2-3 or later
Sambamba v0.7.1 or later
These libraries are called as a processing pipeline by the script satay.sh, which generates a GUI.
Docker
For a full installation and user guide for Docker containers, see our documentation.
The Docker image is hosted at leilaicruz/satay.
Prerequisites:
Windows, macOS, Linux
Docker
Xserver (for displaying the GUI)
To build the image locally in your computer, from DockerHub:
create an account in DockerHub
Pull the image
docker pull leilaicruz/satay:latest
Verify the image is in your computer
docker images
Move to where you have the Dockerfile and build the image
docker build . -t leilaicruz/satay:latest
Move to the location where you have the data you would like to mount to the container, to use $(pwd) in the command bellow (simplest option), otherwise indicate the absolute path from your computer you would like to be loaded.
To run the docker container, use the commands for your Operating System:
# For Windows (and WSL):
docker run --rm -it -e DISPLAY=host.docker.internal:0 -v /$(pwd):/data leilaicruz/satay:latest
# For macOS
docker run --rm -it -e DISPLAY=docker.for.mac.host.internal:0 -v $(pwd):/data leilaicruz/satay
# For Linux
docker run --rm -it --net=host -e DISPLAY=:0 -v $(pwd):/data leilaicruz/satay
The flag -e enables viewing of the GUI outside the container via the Xserver
The flag -v mounts the current directory (pwd) on the host system to the data/ folder inside the container
Troubleshooting
If an error regarding the connection pops up:
Gtk-WARNING **: cannot open display: :0
There is a solution in Linux is typing the following command in the terminal : xhost +
Linux system
Prerequisites:
Anaconda
Python 3.7, 3.8
We recommend installing all dependencies in a conda environment:
git clone https://github.com/SATAY-LL/Transposonmapper.git satay
cd satay
conda env create --file conda/environment-linux.yml
conda activate satay-linux
To start the GUI, simply run
bash satay.sh
Documentation for developers
Installation
To install transposonmapper, do:
git clone https://github.com/SATAY-LL/Transposonmapper.git
cd transposonmapper
conda env create --file conda/environment-dev.yml
conda activate satay-dev
pip install -e .[dev]
Run tests (including coverage) with:
pytest
Docker image
For more information go to our [Jupyter Book](https://satay-ll.github.io/Transposonmapper/03-docker-doc/03-Docker-Developers.html)
Contributing
If you want to contribute to the development of transposonmapper and the SATAY pipeline, have a look at the contribution guidelines.
Contributors
This software is part of the research effort of the LaanLab, Department of BioNanoScience, Delft University of Technology
Leila Iñigo de la Cruz
Gregory van Beek
Maurits Kok
License
Copyright (c) 2020, Technische Universiteit Delft
Licensed under the Apache License, Version 2.0 (the “License”). The 2.0 version of the Apache License, approved by the ASF in 2004, helps us achieve our goal of providing reliable and long-lived software products through collaborative open source software development.
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
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