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. 2021 May 25;22:266. doi: 10.1186/s12859-021-04198-1

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — Comparison of estimated quantification with the truth in simulated data. A, B Scatter plots between the inferred and true counts. Each point represents the average expression of three samples. A Idealized data, B realistic data. C, D Percentiles of the |logFC| (relative to true counts), for the set of expressed isoforms in sample 1 in C idealized and D realistic data. A point (x,y) on a graph means x% of the transcripts have |logFC|< y. For clarity, all unexpressed genes were removed. Unexpressed isoforms were retained if a sibling isoform is expressed. A logFC of 0 means the estimated count is equal to the truth for that isoform. E, F A point on this plot shows the Spearman correlation between the vector of inferred quants and the truth. For each method, the correlation was calculated for each of the three samples, plotted as a box plot. Variation is low, so box plots are thin