For a detailed description of pipeline output, see the documentation
Pipeline outputs are organized into three directories:
| Folder | Description |
|---|---|
| 01_reference_files/ | files that may be of use in other pipelines or analyses |
| 02_intermediate_files/ | large intermediate files, useful when debugging, but otherwise disposable |
| 03_output_files/ | all DNA/RNA probe sets as both .tsv files and zip archives |
All unwanted files can be safely deleted once the pipeline is run.
NOTE: To minimize disk usage, it may be desirable to keep only the three zip archives found in 03_output_files/04_zip_archives/, as the intermediate files are very large (e.g. the pipeline will generate over 200 GB of intermediate files for hg38).
Designed FISH probes are in the following locations:
| Item | Location |
|---|---|
| DNA FISH probes in .tsv format | 03_output_files/01_dna_probes/ |
| Isoform-resolved RNA FISH probes in .tsv format | 03_output_files/02_rna_probes_all/ |
| Isoform-flattened RNA FISH probes in .tsv format | 03_output_files/03_rna_probes_iso/ |
| All DNA/RNA FISH probe sets as compressed .zip archives | 03_output_files/04_zip_archives/ |
An HTML report with diagnostics and detailed pipeline information can by generated with the following command:
$ snakemake --snakefile path/to/Snakefile --configfile path/to/config.yml --report pipeline_output/report.html
An example report is available here. For a visualization of the pipeline DAG structure, see: pipeline.pdf or pipeline.svg
