Overall steps:
Steps in general
- Alignment to get bam
- Filter & dedup bam
- Peak calling to get peaks
Detailed steps
The pipeline for a single paired-end lib contains 15 steps as follow:
- report read length
- alignment
- flagstat bam
- post align: dedup bam
- post align: picard markedup
- post align: dedup bam (again) - final bam file
- post align: name sort bam
- post align: bam to bedpe
- bedpe to tagalign
- shift tagalign
- xcor subset sample
- xcor calculation use subset
- macs2 peak calling
- filter peaks
- ataqc