3. Quickstart

For the impatient, just use portcullis full -t <threads> <genome> (<bam>)+ to get up and running. This runs the following subtools in order:

• Prepare
• Junction Analysis
• Junction Filtering
• Bam Filtering (optional)

This will output both unfiltered and filtered junctions from the provided BAM file. However, we recommend you read the Using Portcullis section for a more detailed description of what each stage does.