Pipelines
      Back to home
      1. Pluto Knowledge Base
      2. Pipelines

      Standard ChIP-seq parameters in Pluto

      Methods for the out-of-the-box ChIP-seq pipeline (nf-core/chipseq)

      Written by Andrew Goodspeed

      Methods

      Raw FASTQ files were processed using the nf-core/chipseq pipeline (v2.0) (1, 2). Adapter sequences were removed with Trim Galore (3). Reads were aligned with STAR (4) to GRCh38/hg19 (human) or GRCm38/mm10 (mouse) and quantified to gene counts using RSEM (5).

      References

      1. Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

      2. doi: 10.5281/zenodo.1400710

      3. https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

      4. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. PubMed PMID: 23104886; PubMed Central PMCID: PMC3530905.

      5. Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome BMC Bioinformatics. 2011 Aug 4;12:323. doi: 10.1186/1471-2105-12-323. PubMed PMID: 21816040; PubMed Central PMCID: PMC3163565.