Fig. 2: Comparison of RNA-seq protocols. | Nature Methods

Fig. 2: Comparison of RNA-seq protocols.

From: A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines

Fig. 2

a, Violin plot showing the median, upper and lower quartiles and 1.5 times the interquartile ranges of the sequencing throughput of RNA (direct RNA, n = 55), cDNA (direct cDNA, n = 30), PCR (cDNA, n = 27), PacBio IsoSeq (n = 6) and Illumina (n = 21) protocols. Circles represent MinION or GridION experimental runs without multiplexing, squares represent PromethION and non-demultiplexed experimental runs, and triangles represent demultiplexed experimental runs. b, Violin plot showing the median, upper and lower quartiles and 1.5 times the interquartile ranges of the average read length per sample of RNA (direct RNA, n = 55), cDNA (direct cDNA, n = 30), PCR (cDNA, n = 27), PacBio IsoSeq (n = 6) and Illumina (n = 21) protocols. Each point represents an experimental run, squares represent PromethION and non-demultiplexed experimental runs, and triangles represent demultiplexed experimental runs. c, Coverage along the normalized transcript length for RNA (direct RNA), cDNA (direct cDNA), PCR (cDNA), PacBio IsoSeq and Illumina protocols. Each light shaded line represents the average across one cell line, and the darker shaded line represents the average across all cell lines for each protocol. d, Box plots showing the median, upper and lower quartiles, and 1.5 times the interquartile ranges of the percentage of reads being uniquely or multi-mapped to transcripts, and whether the read is full-splice-junction matched to the transcript or not (full-splice-match versus partial) for all five protocols (n = 55, 30, 27, 6 and 21 for direct RNA, direct cDNA, cDNA, PacBio and Illumina, respectively). e, Transcription diversity depicted by the percentage of reads attributed to the number of genes ranked by expression levels from highest to lowest for the five protocols. The dashed line represents the top 1,000 expressed genes, and colored numbers indicate the percentage of reads accounted for them. f, Mean read coverage of genes generated using the direct RNA and the PCR cDNA protocol. Each point is colored by the density of genes. Sp.R, Spearman correlation.

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