Overall steps:

Steps in general

  1. Alignment to get bam
  2. Filter & dedup bam
  3. Peak calling to get peaks

Detailed steps

The pipeline for a single paired-end lib contains 15 steps as follow:

  1. report read length
  2. alignment
  3. flagstat bam
  4. post align: dedup bam
  5. post align: picard markedup
  6. post align: dedup bam (again) - final bam file
  7. post align: name sort bam
  8. post align: bam to bedpe
  9. bedpe to tagalign
  10. shift tagalign
  11. xcor subset sample
  12. xcor calculation use subset
  13. macs2 peak calling
  14. filter peaks
  15. ataqc

Reference

  1. ENCODE Standards