Remove duplicates and align the reads to the reference genome using your preferred aligner, ensuring only uniquely mapped reads are retained. If alignment quality is low, repeat the alignment process. 2. Sort and index the BAM files for downstream analysis (optional). 3. Use the BAM files and the corresponding reference genome as input to the RNAEditingIndexer, utilizing a virtual environment or Docker image. 4. For human samples, average on Alu repeats; for mouse samples, use B1 and B2 repeats. If the genome does not have built-in support, prepare the necessary regions, annotations, and SNP files as described in the documentation. 5. Monitor logs and output for errors, adjusting parameters and repeating the alignment process if needed.