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TopHat-Recondition: a post-processor for TopHat unmapped reads

Overview of attention for article published in BMC Bioinformatics, May 2016
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (82nd percentile)
  • High Attention Score compared to outputs of the same age and source (84th percentile)

Mentioned by

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15 X users
wikipedia
1 Wikipedia page

Citations

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11 Dimensions

Readers on

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44 Mendeley
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Title
TopHat-Recondition: a post-processor for TopHat unmapped reads
Published in
BMC Bioinformatics, May 2016
DOI 10.1186/s12859-016-1058-x
Pubmed ID
Authors

Christian Brueffer, Lao H. Saal

Abstract

TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format - the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct format implementation is paramount for software interoperability and correct analysis. However, TopHat writes its unmapped reads in a way that is not compatible with other software that implements the SAM/BAM format. We have developed TopHat-Recondition, a post-processor for TopHat unmapped reads that restores read information in the proper format. TopHat-Recondition thus enables downstream software to process the plethora of BAM files written by TopHat. TopHat-Recondition can repair unmapped read files written by TopHat and is freely available under a 2-clause BSD license on GitHub: https://github.com/cbrueffer/tophat-recondition .

X Demographics

X Demographics

The data shown below were collected from the profiles of 15 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 44 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 5%
Cuba 1 2%
Germany 1 2%
Denmark 1 2%
Sweden 1 2%
Unknown 38 86%

Demographic breakdown

Readers by professional status Count As %
Researcher 17 39%
Student > Ph. D. Student 10 23%
Student > Bachelor 6 14%
Student > Master 2 5%
Student > Doctoral Student 2 5%
Other 4 9%
Unknown 3 7%
Readers by discipline Count As %
Agricultural and Biological Sciences 21 48%
Biochemistry, Genetics and Molecular Biology 10 23%
Computer Science 4 9%
Engineering 2 5%
Medicine and Dentistry 2 5%
Other 1 2%
Unknown 4 9%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 10. 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 07 August 2020.
All research outputs
#3,221,677
of 23,577,761 outputs
Outputs from BMC Bioinformatics
#1,117
of 7,418 outputs
Outputs of similar age
#51,709
of 300,671 outputs
Outputs of similar age from BMC Bioinformatics
#16
of 102 outputs
Altmetric has tracked 23,577,761 research outputs across all sources so far. Compared to these this one has done well and is in the 86th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 7,418 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one has done well, scoring higher than 84% 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 300,671 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 82% of its contemporaries.
We're also able to compare this research output to 102 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 84% of its contemporaries.