(Q31172489)

16 October 2017

Assessment of the impact of using a reference transcriptome in mapping short RNA-Seq reads (English)

1 reference

16 October 2017

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1 reference

1 reference

Shanrong Zhao

1

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PMC publication ID

4081564

16 October 2017

language of work or name

English

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publication date

3 July 2014

1 reference

16 October 2017

1 reference

16 October 2017

9

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16 October 2017

7

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16 October 2017

e101374

1 reference

Creative Commons Attribution 4.0 International

16 October 2017

start time

3 July 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

HTSeq--a Python framework to work with high-throughput sequencing data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Evaluation of alignment algorithms for discovery and identification of pathogens using RNA-Seq

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Systematic evaluation of spliced alignment programs for RNA-seq data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Grape RNA-Seq analysis pipeline environment.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

STAR: ultrafast universal RNA-seq aligner

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Transcriptome analysis using next-generation sequencing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

An introduction to the informatics of "next-generation" sequencing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

RNA-seq: technical variability and sampling.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Microarrays, deep sequencing and the true measure of the transcriptome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Computational methods for transcriptome annotation and quantification using RNA-seq

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Full-length transcriptome assembly from RNA-Seq data without a reference genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer's disease

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

From RNA-seq reads to differential expression results

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Transcriptome genetics using second generation sequencing in a Caucasian population

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Fast and SNP-tolerant detection of complex variants and splicing in short reads

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

RNA-Seq: a method for comprehensive transcriptome analysis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

RNA-Seq: a revolutionary tool for transcriptomics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Mapping and quantifying mammalian transcriptomes by RNA-Seq

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4081564

OSA: a fast and accurate alignment tool for RNA-Seq

14 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0101374

10.1371/JOURNAL.PONE.0101374

21 January 2018

Identifiers

DOI

1 reference

16 October 2017

0 references

1 reference

PMC publication ID

4081564

16 October 2017

PubMed publication ID

24992027

1 reference

PMC publication ID

4081564