Baltica: integrated splice junction usage analysis
- Snakemake workflows for DJU: JunctionSeq, Majiq, rMATS, and Leafcutter
- Snakemake workflow for de novo transcriptome annotation with Stringtie
- Process, integrate and annotate the results from the methods
- Summarise AS class of differently spliced junctions
- DJU method benchmarks
- Report on the integrative analysis
We tested the instruction below in a computer cluster running Debian Linux distribution and using the Slurm job scheduler. Baltica uses Snakemake and Singularity, which support many different high-performance systems, for instructions on how to use it on different systems, please see Setting up Baltica: long edition or contact us,
https://dieterich-lab.github.io/Baltica/.
Feedback and contribution are welcome. Would you mind submitting via the GitHub issue tracker Please provide the following information while submitting issue reports:
- Software and operation system versions
- Command-line call
- If possible, also provide sample data so we can try to reproduce the error