![]() ![]() You want to have as many biological replicates as possible - typically at least 3. Regarding the number of replicates, the Differential Expression for RNA-Seq tool is capable of running without replicates, but this is not recommended and the results should be treated with caution. Both tools use multi-factorial statistics based on a negative binomial Generalized Linear Model (GLM). The Differential Expression for RNA-Seq tool performs a statistical differential expression test for a set of Expression Tracks with associated metadata. The Differential Expression in Two Groups tool performs a statistical differential expression test for a set of Expression Tracks and a set of control tracks. Two tools are available in the Workbench for calculating differential expressions. QIAGEN Digital Insights Team The tools available in QIAGEN CLC Genomics Workbench Premium are compatible both with the Expression Tracks created by the RNA-Seq Analysis tool and the tables created by the miRNA quantification tool. Individual samples can then be combined in downstream differential expression analyses using DESeq2 and we also provide workflows for measuring de novo transcript isoform abundance and differential expression using cufflinks and cuffdiff. We can go from raw reads to RPKM values in about 15 minutes for a typical human dataset, with the ability to process hundreds of samples in parallel. Reads are first aligned to the genome with STAR and then featureCounts is used to measure gene expression at both the gene- and transcript-level. The most commonly used workflow on the Basepair platform provides QC, alignment, and quantification of RNA-seq data. Simon Valentine, Chief Commercial Officer, Basepair How do you perform transcript quantification and also differential expression analysis? ![]()
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