Methods
Raw FASTQ files were processed using the nf-core/rnaseq pipeline (v3.7) (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
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doi: 10.5281/zenodo.1400710
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.
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.