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Considerations and complications of mapping small RNA high-throughput data to transposable elements

Overview of attention for article published in Mobile DNA, February 2017
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (86th percentile)

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Title
Considerations and complications of mapping small RNA high-throughput data to transposable elements
Published in
Mobile DNA, February 2017
DOI 10.1186/s13100-017-0086-z
Pubmed ID
Authors

Alexandros Bousios, Brandon S. Gaut, Nikos Darzentas

Abstract

High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), or when such genomes are large, as is often the case in plants. Here, in an attempt to shed light on complications of mapping sRNAs to TEs, we focus on the 2,300 Mb maize genome, 85% of which is derived from TEs, and scrutinize methodological strategies that are commonly employed in TE studies. These include choices for the reference dataset, the normalization of multiply mapping sRNAs, and the selection among sRNA metrics. We further examine how these choices influence the relationship between sRNAs and the critical feature of TE age, and contrast their effect on low copy genomic regions and other popular HTS data. Based on our analyses, we share a series of take-home messages that may help with the design, implementation, and interpretation of high-throughput TE epigenetic studies specifically, but our conclusions may also apply to any work that involves analysis of HTS data.

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X Demographics

The data shown below were collected from the profiles of 8 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 76 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 1%
United States 1 1%
Netherlands 1 1%
Unknown 73 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 25 33%
Researcher 17 22%
Student > Master 6 8%
Professor > Associate Professor 4 5%
Student > Bachelor 4 5%
Other 8 11%
Unknown 12 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 37 49%
Biochemistry, Genetics and Molecular Biology 21 28%
Computer Science 2 3%
Veterinary Science and Veterinary Medicine 1 1%
Economics, Econometrics and Finance 1 1%
Other 1 1%
Unknown 13 17%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 12. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 16 June 2018.
All research outputs
#2,757,965
of 23,653,133 outputs
Outputs from Mobile DNA
#63
of 341 outputs
Outputs of similar age
#63,846
of 457,509 outputs
Outputs of similar age from Mobile DNA
#1
of 4 outputs
Altmetric has tracked 23,653,133 research outputs across all sources so far. Compared to these this one has done well and is in the 88th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 341 research outputs from this source. They typically receive more attention than average, with a mean Attention Score of 8.3. This one has done well, scoring higher than 81% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 457,509 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 86% of its contemporaries.
We're also able to compare this research output to 4 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them