Trimming of sequence reads alters RNA-Seq gene expression estimates (Q35934860)

11 August 2017

Trimming of sequence reads alters RNA-Seq gene expression estimates (English)

1 reference

11 August 2017

1 reference

1 reference

1

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26911985%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Charles C. Kim

series ordinal

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26911985%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

author name string

Alyssa Baccarella

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26911985%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Jay Z Parrish

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26911985%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

publication date

25 February 2016

1 reference

11 August 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26911985%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

volume

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26911985%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

page(s)

103

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26911985%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

31 May 2020

DESeq2

object named as

R package DESeq2

DESeq2

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

DESeq2

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edgeR

object named as

EdgeR

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

exact match

https://scigraph.springernature.com/pub.10.1186/s12859-016-0956-2

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cites work

Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

A comparative study of techniques for differential expression analysis on RNA-Seq data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Development of the embryonic and larval peripheral nervous system of Drosophila

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Realistic artificial DNA sequences as negative controls for computational genomics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Trimmomatic: a flexible trimmer for Illumina sequence data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

On the optimal trimming of high-throughput mRNA sequence data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

An extensive evaluation of read trimming effects on Illumina NGS data analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Differential analysis of gene regulation at transcript resolution with RNA-seq

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

STAR: ultrafast universal RNA-seq aligner

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Fast gapped-read alignment with Bowtie 2

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

GC-content normalization for RNA-Seq data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

ConDeTri--a content dependent read trimmer for Illumina data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Biases in Illumina transcriptome sequencing caused by random hexamer priming

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

The challenges of sequencing by synthesis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

TopHat: discovering splice junctions with RNA-Seq

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Peripheral multidendritic sensory neurons are necessary for rhythmic locomotion behavior in Drosophila larvae

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Complexity: an internet resource for analysis of DNA sequence complexity

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Global amplification of mRNA by template-switching PCR: linearity and application to microarray analysis.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Amplification of cDNA ends based on template-switching effect and step-out PCR.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Base-calling of automated sequencer traces using phred. II. Error probabilities

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

Comparison of software packages for detecting differential expression in RNA-seq studies

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

New Drosophila transgenic reporters: insulated P-element vectors expressing fast-maturing RFP.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4766705

10.1186/S12859-016-0956-2

24 September 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26911985%20AND%20SRC:MED&resulttype=core&format=json

journals/bmcbi/WilliamsBPK16

31 May 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1018816738

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Fatcat ID

release_2vutjzyci5e27f5nf63bzdimbq

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/2vutjzyci5e27f5nf63bzdimbq

mapped directly with Wikidata item

24 November 2022

based on heuristic

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26911985%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26911985%20AND%20SRC:MED&resulttype=core&format=json