Workflow v2

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Travis Collier edited this page Dec 2, 2015 · 4 revisions

Workflow v2 Notes

data directory structure outline

Species/Reference (eg: AgamP4)
- Sample ID
  - combined
    - combined.bam (and .bai) created from merging all Seq-Runs
    - QC on combined.bam
    - calling = Single-sample variant calling
- Seq-Run #1 (by run ID, eg: BM-cyp1_MOPTI-DNA_Miseq_PE250-01 or YL-GF-09)
  - metadata file containing: Adapters used, ...
  - FASTA
    - raw FASTA [link to archive]
    - trimmed FASTA
  - mapping to reference intermediate files
  - realigned.bam (and .bai)
  - QC on realigned.bam
- Seq-Run #2
  - (same structure as Seq-Run #1)
- … (more Seq-Runs)