lweasel
commented
2 years ago This is an initial text that we could use. Here FILL_THIS_IN indicates something that the paper authors (not us) should fill in, so that can be output verbatim.
"RNA sequencing was performed using FILL_THIS_IN library preparation along with next-generation sequencing on the FILL_THIS_IN platform; sequencing was carried out by FILL_THIS_IN. Samples were sequenced to a depth of approximately <fill - mean reads per sample, rounded to 5 (or 10?) million> million <fill - length of reads in bases>-base pair, <fill - "single-end" or "paired-end"> reads. The reads were mapped to the primary assembly of the <fill - species> (<fill - species genome assembly name, e.g. "mm10", "hg38" etc.>) reference genome contained in Ensembl release <fill - Ensembl version>, using the STAR RNA-seq aligner, version <fill - STAR version> [1]. Tables of per-gene read counts were generated from the mapped reads with featureCounts, version <fill - featureCounts version> [2]. Differential gene expression was performed in R using DESeq2, version <fill - DESeq2 library version> [3]. Gene ontology enrichment analysis was performed using topGO, version <fill - topGO library version> [4]. Gene set testing was then performed using Camera [5] from the R package limma, version <fill - limma library version> [6], using gene sets from the Molecular Signatures Database, version <fill - MSigDb version> (https://www.gsea-msigdb.org/gsea/msigdb/).
[1] Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013). [2] Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014). [3] Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15, 550 (2014). [4] Alexa, A., Rahnenfuhrer, J. & Lengauer, T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22, 1600–1607 (2006). [5] Wu, D. & Smyth, G. K. Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Research 40, e133 (2012). [6] Ritchie et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43, e47 (2015)."
For about the millionth time I've just been writing a methods section for a manuscript, e.g. something like:
and it's really painful every time. I just realised we could produce a text file containing this type of text in cookiecutter, automatically filling in the read-depths, read-lengths, Ensembl and tool version that were associated with that project instance. It doesn't have to be completely the full version that would go into a manuscript, but as a starting point it would save a lot of grief.