examples

Examples

Run these from inside this directory — the paths in each script are relative to it.

cd examples
./splitfastqs_example.sh
./refsplice_example.sh
./count_example.sh
./call_example.sh

splitfastqs_example.sh splits the bundled sample FASTQ into one file per barcode. The other three scripts do not consume its output. The aligned perturbed BAMs are already checked in under example_data/TX46_Prosalpha3_bams/, so the analysis runs without repeating the alignment step. All three share --results-dir=results and the run name TX46_Prosalpha3, and write into results/.

Two notes:

• count_example.sh writes a mutations/ directory inside example_data/TX46_Prosalpha3_bams/, which is part of the tree. Delete it after a run.
• The final results/TX46_Prosalpha3_mutation_statuses.txt should match the checked-in example_data/ref_TX46_Prosalpha3_mutation_statuses.txt. The reference file's rows are in a different order, so compare with sort on both sides.

For a walkthrough of what each stage does and how to adapt this to your own data, see ../docs/tutorial.md.