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Deep Sequencing Data Analysis

Overview of attention for book
Cover of 'Deep Sequencing Data Analysis'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 An Introduction to High-Throughput Sequencing Experiments: Design and Bioinformatics Analysis
  3. Altmetric Badge
    Chapter 2 Compressing Resequencing Data with GReEn
  4. Altmetric Badge
    Chapter 3 On the Accuracy of Short Read Mapping
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    Chapter 4 Statistical Modeling of Coverage in High-Throughput Data
  6. Altmetric Badge
    Chapter 5 Assembly Algorithms for Deep Sequencing Data: Basics and Pitfalls
  7. Altmetric Badge
    Chapter 6 Short Read Mapping for Exome Sequencing
  8. Altmetric Badge
    Chapter 7 Profiling Short Tandem Repeats from Short Reads
  9. Altmetric Badge
    Chapter 8 Exome sequencing analysis: a guide to disease variant detection.
  10. Altmetric Badge
    Chapter 9 Identifying RNA Editing Sites in miRNAs by Deep Sequencing
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    Chapter 10 Identifying Differential Alternative Splicing Events from RNA Sequencing Data Using RNASeq-MATS.
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    Chapter 11 Optimizing Detection of Transcription Factor-Binding Sites in ChIP-seq Experiments
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    Chapter 12 Statistical Analysis of ChIP-seq Data with MOSAiCS
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    Chapter 13 Detection of Reverse Transcriptase Termination Sites Using cDNA Ligation and Massive Parallel Sequencing
Attention for Chapter 13: Detection of Reverse Transcriptase Termination Sites Using cDNA Ligation and Massive Parallel Sequencing
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Chapter title
Detection of Reverse Transcriptase Termination Sites Using cDNA Ligation and Massive Parallel Sequencing
Chapter number 13
Book title
Deep Sequencing Data Analysis
Published in
Methods in molecular biology, January 2013
DOI 10.1007/978-1-62703-514-9_13
Pubmed ID
23872978
Book ISBNs
978-1-62703-513-2, 978-1-62703-514-9
Authors

Lukasz J. Kielpinski, Mette Boyd, Albin Sandelin, Jeppe Vinther, Kielpinski, Lukasz J., Boyd, Mette, Sandelin, Albin, Vinther, Jeppe

Abstract

Detection of reverse transcriptase termination sites is important in many different applications, such as structural probing of RNAs, rapid amplification of cDNA 5' ends (5' RACE), cap analysis of gene expression, and detection of RNA modifications and protein-RNA cross-links. The throughput of these methods can be increased by applying massive parallel sequencing technologies.Here, we describe a versatile method for detection of reverse transcriptase termination sites based on ligation of an adapter to the 3' end of cDNA with bacteriophage TS2126 RNA ligase (CircLigase™). In the following PCR amplification, Illumina adapters and index sequences are introduced, thereby allowing amplicons to be pooled and sequenced on the standard Illumina platform for genomic DNA sequencing. Moreover, we demonstrate how to map sequencing reads and perform analysis of the sequencing data with freely available tools that do not require formal bioinformatics training. As an example, we apply the method to detection of transcription start sites in mouse liver cells.

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 Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 17 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 6%
Denmark 1 6%
Germany 1 6%
Unknown 14 82%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 5 29%
Researcher 3 18%
Student > Bachelor 2 12%
Student > Master 2 12%
Student > Doctoral Student 1 6%
Other 3 18%
Unknown 1 6%
Readers by discipline Count As %
Agricultural and Biological Sciences 9 53%
Biochemistry, Genetics and Molecular Biology 8 47%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 08 November 2013.
All research outputs
#18,353,475
of 22,729,647 outputs
Outputs from Methods in molecular biology
#7,855
of 13,086 outputs
Outputs of similar age
#218,076
of 280,769 outputs
Outputs of similar age from Methods in molecular biology
#220
of 341 outputs
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So far Altmetric has tracked 13,086 research outputs from this source. They receive a mean Attention Score of 3.3. This one is in the 24th percentile – i.e., 24% of its peers scored the same or lower than it.
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We're also able to compare this research output to 341 others from the same source and published within six weeks on either side of this one. This one is in the 12th percentile – i.e., 12% of its contemporaries scored the same or lower than it.

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