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. 2021 May 31;22:290. doi: 10.1186/s12859-021-04208-2

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© The Author(s) 2021, corrected publication 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. 5 — Comparison of called yeast genes to SacCer3. A Distribution of differences between 5' or 3' borders (left and right panels, respectively) of the matched gene pairs. Y axis shows the number of gene pairs, X axis shows the difference of genomic coordinates (in bp). A negative (positive) difference value means that the border of the called gene is located upstream (downstream) from the respective border of its mate in SacCer3. B Metagene profile of TSS-seq signal over 5' gene borders on matched HC/SacCer3 gene pairs. Fixed length genomic intervals (200 bp) were centered on the 5' gene borders predicted by either TranscriptomeReconstructoR or SacCer3. Y axis shows the average sequencing coverage of TSS-seq, X axis shows the genomic coordinates relative to the 5' gene border (zero corresponds to the predicted gene start). Color of the wiggle line indicates the origin of the genomic windows: blue for SacCer3 and red for the called HC genes. C Metagene profile of 3' mRNA-seq signal over 3' gene borders on matched HC/SacCer3 gene pairs. D Metagene plot of NET-seq signal over the whole bodies of novel HC, MC and LC genes and novel transient RNAs. The genes were scaled to 100 bins. The 100 bp upstream and downstream flanking regions were scaled to 20 bins each. The vertical lines in the plotting area denote the starts and ends of novel genes. Red and blue wiggle lines show the average RNAPII elongation activity in novel genes and transient RNAs, respectively. Red and blue shaded areas show normal-bases 95% confidence interval for the respective means