Scripts used for generating long-read RNA fusion transcripts for testing and benchmarking my fusion detection algorithm. Simulator I used: Badread.

Example:

python3 known_fusions_to_spec.py \
  --gtf ~/Thesis/refs/gencode.v49.primary_assembly.annotation.gtf \
  --pairs ~/LongReadSimulation/known_fusions.txt \
  --out ~/My_simulation/fusions_spec.tsv \
  --n 500 \
  --seed 123 \
  --primary_only

python3 make_fusion_transcripts.py \
  --gtf ~/Thesis/refs/gencode.v49.primary_assembly.annotation.gtf  \
  --fasta ~/Thesis/refs/GRCh38.primary_assembly.genome.fa \
  --spec ~/My_simulation/fusions_spec.tsv \
  --outdir ~/My_simulation/fusion_ont \
  --protein_coding_only \
  --tag_basic_only

Combine the output FASTA with a reference transcriptome or a part of it. Use the combined file as a reference for the simulator.

badread simulate \
  --reference combined_reference.fa \
  --quantity 10x \
  --error_model nanopore2023 \
  --junk_reads 0.1 \
  --random_reads 0.1 \
  --chimeras 0.1 \
  | gzip > my_ont_reads.fastq.gz