3. QuickstartΒΆ
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.