Fig. 2
From: Limitations of alignment-free tools in total RNA-seq quantification
Gene detection and quantification. a Numbers and types of detected genes in every sample and pipeline. Genes with TPM>0.1 were labeled as being detected. The stacked bar charts indicate the numbers of genes detected by each pipeline. The bar charts are grouped by library (A1–D3), where A–D represent the RNA samples and the numbers represent replicate identifiers. The stacked-bars are color-coded by RNA type. b ERCC spike-in quantifications versus the true spike-in abundances. Log2 transcripts per million (TPM) values for every ERCC transcript from every replicate are plotted against the known spike-in concentrations, grouped by pipelines and samples. Blue lines indicate least-square regression lines. Coefficients of determination are annotated in each panel