Package: transposonmapper
SATAY and TransposonmapperThis 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, seethe satay user websitecreated 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 trimmingquality checking raw and trimmed fastq filessequence alignment with reference genome (S288C Cerevisiae genome)quality checking bam files, indexing and sortingtransposon mappingThe 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.Badgesfair-software.nl recommendations1. Code repository2. License3. Community Registry4. Enable Citation5. ChecklistsCode quality checksContinuous integrationDocumentationCode QualityDocumentation for usersPyPI packageFor users that only require post processing analysis of the data (the bam file was already analyzed),
do use the default installation. For examplepysamwon’t be installed, hence Linux is not required.pip install transposonmapperFor users that require the whole processing pipeline, do use:pip install transposonmapper[linux]For more extensive documentation,see our JupyterBook.SATAY pipelineWe 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:FASTQCv0.11.9 or laterBBMapv38.87 or laterTrimmomaticv0.39 or laterBWAv0.7.17 or laterSAMToolsv1.10 or laterBCFToolsv1.10.2-3 or laterSambambav0.7.1 or laterTransposonmapperThese libraries are called as a processing pipeline by the scriptsatay.sh,
which generates a GUI.Preprocessing stepsBefore inputting the data into the satay pipeline, it is necessary to preprocess the data that comes from the sequencing company.The pipeline does not process each digestion separately and therefore any pre-processing and trimming of the restriction sites should be donepriorto running the pipeline.What we do if the sequencing data is paired end:If the data is paired end, only one of the pairs will map to the transposon insertion site (the end that has been sequenced from the sequencing primer), while the other end will map back to a location arbitrarily far upstream or downstream of the insertion site (depends on where the restriction site is).Preprocessing steps prior to use the satay pipeline:Convert the data to single end by:Extracting the forward reads, which are the reads that contain the sequencing primer, as it is (harsh filtering) or allowing some mismatches in the sequencing primer, due to likely sequencing errors (gentle filtering).Remove the sequence downstream the first restriction site for NiaIII and DpnII to avoid having chimeras sequences in our data, that have poor alignment.Discard reads bellow 50bp after trimming of the restriction site to ensure a decent confidence alignment score for that read.DockerFor a full installation and user guide for Docker containers,see our documentation.The Docker image is hosted atleilaicruz/satay.Prerequisites:Windows, macOS, LinuxDockerXserver (for displaying the GUI)To build the image locally in your computer, from DockerHub:create an account in DockerHubPull the imagedocker pull leilaicruz/satay:latestVerify the image is in your computerdocker imagesMove to where you have the Dockerfile and build the imagedocker build . -t leilaicruz/satay:latestMove to the location where you have the data you would like to mount to the container, to use$(pwd)in the command bellow (simplest option), otherwise indicate the absolute path from your computer you would like to be loaded.To run the docker container, use the commands for your Operating System:#ForWindows(andWSL):docker run --rm -it -e DISPLAY=host.docker.internal:0 -v /$(pwd):/data leilaicruz/satay:latest#FormacOSdocker run --rm -it -e DISPLAY=docker.for.mac.host.internal:0 -v $(pwd):/data leilaicruz/satay#ForLinuxdocker run --rm -it --net=host -e DISPLAY=:0 -v $(pwd):/data leilaicruz/satayThe flag-eenables viewing of the GUI outside the container via the XserverThe flag-vmounts the current directory (pwd) on the host system to thedata/folder inside the containerTroubleshootingIf an error regarding the connection pops up:Gtk-WARNING **: cannot open display: :0There is a solution in Linux is typing the following command in the terminal :xhost +Linux systemPrerequisites:AnacondaPython 3.7, 3.8We 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-linuxTo start the GUI, simply runbash satay.shDocumentation for developersInstallationTo 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:pytestDocker imageFor more information go to our [Jupyter Book](https://satay-ll.github.io/Transposonmapper/03-docker-doc/03-Docker-Developers.html)ContributingIf you want to contribute to the development of transposonmapper and the SATAY pipeline,
have a look at thecontribution guidelines.ContributorsThis software is part of the research effort of theLaanLab,
Department of BioNanoScience, Delft University of TechnologyLeila Iñigo de la CruzGregory van BeekMaurits KokLicenseCopyright (c) 2020, Technische Universiteit DelftLicensed 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.