Experiment Pipeline Methods
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      2. Experiment Pipeline Methods

      Standard PRO-seq parameters in Pluto

      Methods for the out-of-the-box PRO-seq pipeline

      Written by Andrew Goodspeed

      Methods

      Raw FASTQ files were processed using the nf-core/nascent pipeline (1, 2). Reads were aligned with BWA (4) to GRCh38/hg19 (human) or GRCm38/mm10 (mouse) and quantified to gene counts using featureCounts (5) and a custom SAF file.

      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.