Long-read sequencing has become an increasingly popular tool for RNA sequencing that provides unprecedented insight into isoform, translocation and variant calling analysis.
Further documentation and tutorial on how to run a workflow can be found at read the docs here
TallyTriN is a collection of bulk and single-cell workflows that utilize Unique Molecular Identifiers (UMIs) synthesized using trimer blocks of nucleotides.
Included within this repo are the follwing workflows:
- pipeline_count - a bulk RNA-seq workflow that facilitates the analysis of UMIs synthesised using trimer nucleoside blocks added to the 5' and 3' of the RNA molecule.
- pipeline_fusion - a bulk analysis pipeline for the analysis of fusion transcripts. It implements a strategy for removing chimeric artefacts and quantifies real genomic translocation at the RNA-seq level.
- pipeline_singlecell - a workflow that facilitates the analysis of scCOLOR-seq nanopore single-cell sequencing data, but with trimers added at the 5' end of the RNA.
- pipeline_10X - a workflow that facilitates the analysis of 10X sequencing data.
We reccomend installing miniconda, then creating a new environment and install mamba. This istallation typically takes 10 minutes.
conda install mamba -c conda-forge
Next install the required software using the conda yml file
# Clone the TallyTriN repo
git clone https://github.com/cribbslab/TallyTriN.git
# Use mamba to install environment
mamba env update --file conda/environment.yml
Activate the condda environment
conda activate tallytrin
Then, you will need to manually install TallyTriN and the fork of umi tools. The fork is added as a submodule to this repo to help you easily install.
# Install TallyTriN code
python setup.py install
Further information how you can run the pipelines can be found at read the docs
Run the tallytrin --help command to see what workflows are available and tallytrin count -help to see how to use them.
For example, to generate a configuration file run
tallytrin count config
To set up the configuration file, please refer to our documentation.
To run the pipeline with all tasks, run
tallytrin count make full -v5
The bioRxiv manuscript accompanying this code can be found here:
https://www.biorxiv.org/content/10.1101/2023.04.06.535911v1