[Describe here what this pipeline does]
This pipeline can be run using each of the following container methods
Method | Instructions |
---|---|
Singularity | docs.syslabs.io |
Docker | docs.docker.com |
Conda | docs.conda.io |
sudo singularity build singularity/pipeline Singularity
Then as the profile singularity
specifies container = 'singularity/pipeline'
use the following to execute:
nextflow run main.nf -profile singularity
docker build . -t pipeline-image
Then as the profile docker
specifies container = 'pipeline-image:latest'
use the following to execute:
nextflow run main.nf -profile docker
Create a conda definition yaml file eg. here
nextflow run main.nf -profile conda
Call the pipeline directly
nextflow run main.nf
Run with all the frills
bash scripts/run-w-frills <params-file> <profile name from nextflow.config>
Example
bash scripts/run-w-frills example_parameters.yml standard
Data Processing For RiboSeq.org
This is a set of resources for the analysis and visualisation of publically available ribosome profiling data produced and maintained by various members of LAPTI lab in the School of Biochemistry and Cell Biology at Univeristy College Cork. These resources are well documented in their respective publications
-
GWIPS-Viz
- GWIPS-viz: 2018 update (2018). Nucleic Acids Res
- The GWIPS-viz Browser (2018). Current Protocols in Bioinformatics
- GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms (2015). Proteomics
- GWIPS-viz: development of a ribo-seq genome browser (2014). Nucleic Acids Res
-
Trips-Viz: a transcriptome browser for exploring Ribo-Seq data (2019). Nucleic Acids Res
-
RiboGalaxy: a browser based platform for the alignment, analysis and visualization of ribosome profiling data. RNA Biology-Viz
- ** Note: Ribogalaxy is being updated currently and functionality will be restored shortly (14-2-2022)**
- Produce Database Of All Available Ribosome Profiling Studies
- Gather Metadata
- Fetch Files and Infer Gaps in Metadata
- Run Pipeline
- Upload to GWIPS & TRIPS
In recent years the rate at which ribosome profiling studies have been published has steadily increased. When the riboseq.org resources were initiatlly developed the number of available ribo-seq datasets was managable via manual inclusion. Here we put in place a method that records the details of relevant ribosome profiling data deposited in GEO
Initially manual searching of GEO and SRA were used along with ARGEOS. The outputs of each of these methods were colated to find the set of unique datasets.
GEO and SRA run tables contain valuable metadata that may be important for the processing and cateloging of the datasets. In this step we use python scripts to glean what we can from the information available
A common problem with reprocessing data for these resources is that the data is deposited in GEO and SRA with inconsistent metadata. In the stage of the process we carry out a number of steps to check for the relevant data in the provided metadata and where it is absent we infer it from the data itself. This relates to information such as cell type and treatment but also UMI position and adapter position/sequence.
In this stage we use nextflow to process the fetched reads following the schema below
This stage uses the metadata to upload the processed files to the web resources in an automated fashion