Best practices for RNA-seq
Chen JW et al (2023). The hitchhikers’ guide to RNA sequencing and functional analysis. Briefings in Bioinformatics 24:bbac529.
Conesa A et al (2016). A survey of best practices for RNA-seq data analysis. Genome Biology 17:13.
Sims D et al (2014). Sequencing depth and coverage: key considerations in genomic analyses. Nature Reviews Genetics 15:121-132.
Liu Y, Zhou J, White KP (2014). RNA-seq differential expression studies: more sequence or more replication? Bioinformatics 30:301-304.
Best practices for single-cell RNA-seq
Grones C et al (2024). Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics. Plant Cell. 36:812-828.
Van de Sande B et al (2023). Applications of single-cell RNA sequencing in drug discovery and development. Nat Rev Drug Discov. 22:496-520.
Heumos L et al (2023). Best practices for single-cell analysis across modalities. Nat Rev Genet. 24:550-572.
Luecken MD, Theis FJ (2019). Current best practices in single-cell RNA-seq analysis. Mol Syst Biol. 15:e8746.
Lafzi et al (2018). Guidelines for the experimental design of single-cell RNA sequencing studies. Nature Protocols 13:2742-2757.
Haque A et al (2017). A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Medicine 9:75.
Bacher R, Kendziorski C (2016). Design and computational analysis of single-cell RNA-sequencing experiments. Genome Biology 17:63.
Best practices for circular RNA-seq
Dance A (2024). Circular logic: understanding RNA’s strangest form yet. Nature 635:511-513.
Nielsen AF et al (2022). Best practice standards for circular RNA research. Nature Methods 19:1208-1220
Dodbele S et al (2021). Best practices to ensure robust investigation of circular RNAs: pitfalls and tips. EMBO Reports 22:e52072.
Best practices for Ribo-seq
Ingolia NT, Hussmann JA, Weissman JS. (2019). Ribosome Profiling: Global Views of Translation. Cold Spring Harb Perspect Biol. 11(5):a032698.
Calviello L, Ohler U (2017). Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome. Trends Genetics 33:728-744.
Ingolia NT (2016). Ribosome Footprint Profiling of Translation throughout the Genome. Cell 165:22-33.
Best practices for ATAC-seq
Grandi FC, Modi H, Kampman L, Corces MR (2022). Chromatin accessibility profiling by ATAC-seq. Nature Protocols 17:1518-1552.
Best practices for ChIP-seq
Bailey T et al (2013). Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Computational Biology 9:e1003326.
Landt SG et al (2012). ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research 22:1813-1831.
Best practices for Genome-seq, Exome-seq, Targeted re-sequencing
Xiao W et al (2021). Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing. Nature Biotechnology 39:1141-1150.
Koboldt DC (2020). Best practices for variant calling in clinical sequencing. Genome Medicine 12:91.
