(Q39424417)

11 September 2017

title

Rail-RNA: scalable analysis of RNA-seq splicing and coverage (English)

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11 September 2017

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Andrew E Jaffe

3

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Jeffrey T. Leek

8

object named as

Jeffrey T Leek

1 reference

11 September 2017

9

Ben Langmead

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11 September 2017

1

Abhinav Nellore

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11 September 2017

author name string

Leonardo Collado-Torres

2

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11 September 2017

José Alquicira-Hernández

4

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11 September 2017

Christopher Wilks

5

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11 September 2017

Jacob Pritt

6

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11 September 2017

James Morton

7

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11 September 2017

language of work or name

English

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publication date

4 September 2016

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11 September 2017

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Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols

11 September 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

HISAT: a fast spliced aligner with low memory requirements

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

Developmental regulation of human cortex transcription and its clinical relevance at single base resolution

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

Differential expression analysis of RNA-seq data at single-base resolution

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

Transcriptome and genome sequencing uncovers functional variation in humans

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

The Genotype-Tissue Expression (GTEx) project

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

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

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

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

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

CRAC: an integrated approach to the analysis of RNA-seq reads

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

STAR: ultrafast universal RNA-seq aligner

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

The GEM mapper: fast, accurate and versatile alignment by filtration

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

Modelling and simulating generic RNA-Seq experiments with the flux simulator

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

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

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

A context-based approach to identify the most likely mapping for RNA-seq experiments

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

Fast gapped-read alignment with Bowtie 2

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

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

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

Field guide to next-generation DNA sequencers

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

RNA sequencing: advances, challenges and opportunities

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

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

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

BigWig and BigBed: enabling browsing of large distributed datasets

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

Cloud computing and the DNA data race

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

The case for cloud computing in genome informatics

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

Supersplat--spliced RNA-seq alignment

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

Detection of splice junctions from paired-end RNA-seq data by SpliceMap.

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

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

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

The Sequence Alignment/Map format and SAMtools

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

TopHat: discovering splice junctions with RNA-Seq

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

RNA-Seq: a revolutionary tool for transcriptomics

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

The human genome browser at UCSC

1 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

Optimal spliced alignments of short sequence reads

1 October 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW575

Improvements to services at the European Nucleotide Archive

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW575

IPython: A System for Interactive Scientific Computing

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTW575

RNA-Seq Read Alignments with PALMapper

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5860083

10.1093/BIOINFORMATICS/BTW575

2 December 2018

Identifiers

DOI

0 references

DBLP publication ID

journals/bioinformatics/NelloreCJAWPMLL17

1 reference

DBLP Dataset 2021-01-02

28 January 2021

PMC publication ID

5860083

0 references

1 reference