.. _readings: Assigned Reading ======================================== Biology ---------------------------------------- - `Quantitative bacterial transcriptomics with RNA-seq `_ - `Studying bacterial transcriptomes using RNA-seq `_ - `Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes `_ - `pH Regulates Genes for Flagellar Motility, Catabolism, and Oxidative Stress in Escherichia coli K-12† `_ Statistics ---------------------------------------- - `Statistical Design and Analysis of RNA Sequencing Data `_ - `Statistical Challenges in Preprocessing in Microarray Experiments in Cancer `_ - `Statistical Considerations for Analysis of Microarray Experiments `_ - `Differential expression analysis for sequence count data `_ Bioinformatics ---------------------------------------- - `Ultrafast and memory-efficient alignment of short DNA sequences to the human genome `_ - `Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples `_ - `Fast gapped-read alignment with Bowtie 2 `_ - `TopHat: discovering splice junctions with RNA-Seq `_ - `Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 `_