Lognormality and oscillations in the coverage of high-throughput transcriptomic data towards gene ends

DOI10.1088/1742-5468/2013/10/P10013zbMATH Open1456.92055arXiv1303.4229OpenAlexW3102375067MaRDI QIDQ3301424FDOQ3301424

Authors: Nicolas Innocenti, Erik Aurell 

Publication date: 11 August 2020

Published in: Journal of Statistical Mechanics: Theory and Experiment (Search for Journal in Brave)

Abstract: High-throughput transcriptomics experiments have reached the stage where the count of the number of reads alignable to a given position can be treated as an almost-continuous signal. This allows to ask questions of biophysical/biotechnical nature, but which may still have biological implications. Here we show that when sequencing RNA fragments from one end, as it is the case on most platforms, an oscillation in the read count is observed at the other end. We further show that these oscillations can be well described by Kolmogorov's 1941 broken stick model. We investigate how the model can be used to improve predictions of gene ends (3' transcript ends) but conclude that with present data the improvement is only marginal. The results highlight subtle effects in high-throughput transcriptomics experiments which do not have a biological origin, but which may still be used to obtain biological information.

Full work available at URL: https://arxiv.org/abs/1303.4229

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Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40)

Cites Work

• Moments of particle size distributions under sequential breakage with applications to species abundance

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