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A survey of best practices for RNA-seq data analysis

Overview of attention for article published in Genome Biology (Online Edition), January 2016
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • Among the highest-scoring outputs from this source (#29 of 3,968)
  • High Attention Score compared to outputs of the same age (99th percentile)

Mentioned by

news
1 news outlet
blogs
4 blogs
twitter
427 tweeters
patent
3 patents
facebook
11 Facebook pages
wikipedia
10 Wikipedia pages
googleplus
3 Google+ users
reddit
1 Redditor
video
1 video uploader

Citations

dimensions_citation
1464 Dimensions

Readers on

mendeley
9719 Mendeley
citeulike
31 CiteULike
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Title
A survey of best practices for RNA-seq data analysis
Published in
Genome Biology (Online Edition), January 2016
DOI 10.1186/s13059-016-0881-8
Pubmed ID
Authors

Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, Ali Mortazavi

Abstract

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.

Twitter Demographics

The data shown below were collected from the profiles of 427 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 9,719 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 76 <1%
United Kingdom 25 <1%
Germany 19 <1%
Brazil 17 <1%
Spain 13 <1%
Sweden 9 <1%
Mexico 9 <1%
France 7 <1%
Italy 7 <1%
Other 94 <1%
Unknown 9443 97%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 2611 27%
Researcher 1722 18%
Student > Master 1451 15%
Student > Bachelor 929 10%
Student > Doctoral Student 559 6%
Other 1197 12%
Unknown 1250 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 3216 33%
Biochemistry, Genetics and Molecular Biology 3027 31%
Medicine and Dentistry 372 4%
Computer Science 350 4%
Immunology and Microbiology 270 3%
Other 969 10%
Unknown 1515 16%

Attention Score in Context

This research output has an Altmetric Attention Score of 281. 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 21 June 2022.
All research outputs
#91,201
of 21,429,365 outputs
Outputs from Genome Biology (Online Edition)
#29
of 3,968 outputs
Outputs of similar age
#1,789
of 374,183 outputs
Outputs of similar age from Genome Biology (Online Edition)
#1
of 1 outputs
Altmetric has tracked 21,429,365 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 99th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,968 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 27.6. This one has done particularly well, scoring higher than 99% 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 374,183 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 99% of its contemporaries.
We're also able to compare this research output to 1 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