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2017年的一个转录组综合性分析流程-hppRNA

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发表于 2017-4-20 10:20:15 | 显示全部楼层 |阅读模式
不仅仅是差异表达分析,还囊括了the identification of fusion genes, single nucleotide polymorphisms, long noncoding RNAs and circular RNAs!
文章地址是:https://www.ncbi.nlm.nih.gov/pubmed/28096075hppRNA-a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples.
流程模块如下:

核心流程是6个:
Tophat-Cufflink-Cuffdiff
Subread-featureCounts-DESeq2
STAR-RSEM-EBSeq
Bowtie-eXpress-edgeR
kallisto-sleuth
HISAT-StringTie-Ballgown
发表上面这些工具的文章是:
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31.Trapnell C, Williams BA, Pertea G, et al. Transcript assembly
and quantification by RNA-Seq reveals unannotated transcripts
and isoform switching during cell differentiation. Nat
Biotechnol 2010;28:511–15.
32.Kim D, Pertea G, Trapnell C, et al. TopHat2: accurate alignment
of transcriptomes in the presence of insertions, deletions
and gene fusions. Genome Biol 2013;14:R36.
33.Trapnell C, Hendrickson DG, Sauvageau M, et al. Differential
analysis of gene regulation at transcript resolution with RNAseq.
Nat Biotechnol 2013;31:46–53.
34.Liao Y, Smyth GK, Shi W. featureCounts: an efficient general
purpose program for assigning sequence reads to genomic
features. Bioinformatics 2014;30:923–30.
35.Love MI, Huber W, Anders S. Moderated estimation of fold
change and dispersion for RNA-seq data with DESeq2.
Genome Biol 2014;15:550.
36.Liao Y, Smyth GK, Shi W. The subread aligner: fast, accurate
and scalable read mapping by seed-and-vote. Nucleic Acids Res
2013;41:e108.
37.Leng N, Dawson JA, Thomson JA, et al. EBSeq: an empirical
Bayes hierarchical model for inference in RNA-seq experiments.
Bioinformatics 2013;29:1035–43.
38.Li B, Dewey CN. RSEM: accurate transcript quantification
from RNA-Seq data with or without a reference genome. BMC
Bioinformatics 2011;12:323.
39.Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal
RNA-seq aligner. Bioinformatics 2013;29:15–21.
40.Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor
package for differential expression analysis of digital gene
expression data. Bioinformatics 2010;26:139–40.
41.Langmead B, Salzberg SL. Fast gapped-read alignment with
Bowtie 2. Nat Methods 2012;9:357–9.
42.Roberts A, Pachter L. Streaming fragment assignment for
real-time analysis of sequencing experiments. Nat Methods
2013;10:71–3.
43.Pimentel HJ, Bray N, Puente S, et al. Differential analysis of
RNA-Seq incorporating quantification uncertainty. bioRxiv
2016:058164.
44.Bray NL, Pimentel H, Melsted P, et al. Near-optimal
probabilistic RNA-seq quantification. Nat Biotechnol
2016;34:525–7.
45.Frazee AC, Pertea G, Jaffe AE, et al. Ballgown bridges the gap
between transcriptome assembly and expression analysis.
Nat Biotechnol 2015;33:243–6.
46.Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced
aligner with low memory requirements. Nat Methods
2015;12:357–60.
47.Pertea M, Pertea GM, Antonescu CM, et al. StringTie enables
improved reconstruction of a transcriptome from RNA-seq
reads. Nat Biotechnol 2015;33:290–5


细数了以前发表的22个流程的不足,分别是Chipster, wapRNA, PRADA, RseqFlow and RobiNA,RSEQtools,TRAPLINE ,TCW,ArrayExpressHTS and easyRNASeq,NGSUtils, ViennaNGS and S-MART ,RAP and FX ,QuickNGS ,ExpressionPlot ,GeneProf ,GenomeSpace ,Galaxy
发表这些流程的文章是:
[AppleScript] 纯文本查看 复制代码
5. Kallio MA, Tuimala JT, Hupponen T, et al. Chipster: userfriendly
analysis software for microarray and other highthroughput
data. BMC Genomics 2011;12:507.
6. Torres-Garcia W, Zheng S, Sivachenko A, et al. PRADA: pipeline
for RNA sequencing data analysis. Bioinformatics
2014;30:2224–6.
7. Lohse M, Bolger AM, Nagel A, et al. RobiNA: a user-friendly,
integrated software solution for RNA-Seq-based transcriptomics.
Nucleic Acids Res 2012;40:W622–7.
8. Wang Y, Mehta G, Mayani R, et al. RseqFlow: workflows for
RNA-Seq data analysis. Bioinformatics 2011;27:2598–600.
9. Zhao W, Liu W, Tian D, et al. wapRNA: a web-based application
for the processing of RNA sequences. Bioinformatics
2011;27:3076–7.
10.Habegger L, Sboner A, Gianoulis TA, et al. RSEQtools: a modular
framework to analyze RNA-Seq data using compact, anonymized
data summaries. Bioinformatics 2011;27:281–3.
11.Wolfien M, Rimmbach C, Schmitz U, et al. TRAPLINE: a standardized
and automated pipeline for RNA sequencing data analysis,
evaluation and annotation. BMC Bioinformatics 2016;17:21.
12.Delhomme N, Padioleau I, Furlong EE, et al. easyRNASeq: a
bioconductor package for processing RNA-Seq data.
Bioinformatics 2012;28:2532–3.
13.Goncalves A, Tikhonov A, Brazma A, et al. A pipeline for RNAseq
data processing and quality assessment. Bioinformatics
2011;27:867–9.
14.Breese MR, Liu Y. NGSUtils: a software suite for analyzing
and manipulating next-generation sequencing datasets.
Bioinformatics 2013;29:494–6.
15.Zytnicki M, Quesneville H. S-MART, a software toolbox to aid
RNA-Seq data analysis. PLoS One 2011;6:e25988.
16.Wolfinger MT, Fallmann J, Eggenhofer F, et al. ViennaNGS: a
toolbox for building efficient next- generation sequencing
analysis pipelines. F1000Res 2015;4:50.
17.Cumbie JS, Kimbrel JA, Di Y, et al. GENE-counter: a computational
pipeline for the analysis of RNA-Seq data for gene expression
differences. PLoS One 2011;6:e25279.
18.Hong D, Rhie A, Park SS, et al. FX: an RNA-Seq analysis tool on
the cloud. Bioinformatics 2012;28:721–3.
19.D’Antonio M, D’Onorio De Meo P, Pallocca M, et al. RAP: RNASeq
analysis pipeline, a new cloud-based NGS web application.
BMC Genomics 2015;16:S3.
20.Kartashov AV, Barski A. BioWardrobe: an integrated platform
for analysis of epigenomics and transcriptomics data. Genome
Biol 2015;16:158.
21.Wagle P, Nikolic M, Frommolt P. QuickNGS elevates nextgeneration
sequencing data analysis to a new level of automation.
BMC Genomics 2015;16:487.
22.Friedman BA, Maniatis T. ExpressionPlot: a web-based framework
for analysis of RNA-Seq and microarray gene expression
data. Genome Biol 2011;12:R69.
23.Halbritter F, Kousa AI, Tomlinson SR. GeneProf data: a resource
of curated, integrated and reusable high-throughput
genomics experiments. Nucleic Acids Res 2014;42:D851–8.
24.Halbritter F, Vaidya HJ, Tomlinson SR. GeneProf: analysis of
high-throughput sequencing experiments. Nat Methods
2011;9:7–8.
25.Qu K, Garamszegi S, Wu F, et al. Integrative genomic analysis
by interoperation of bioinformatics tools in GenomeSpace.
Nat Methods 2016;13:245–7.
26.Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive
approach for supporting accessible, reproducible, and transparent
computational research in the life sciences. Genome
Biol 2010;11:R86.



你这个问题很复杂,需要打赏,请点击 http://www.bio-info-trainee.com/donate 进行打赏,谢谢
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发表于 2017-4-20 10:35:19 | 显示全部楼层
先马后看,看起来很全面的样子
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发表于 2017-4-20 11:07:10 | 显示全部楼层
静静的学习中
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发表于 2017-4-27 17:12:15 | 显示全部楼层
这篇文章看过,不过没有总结得这么详细
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发表于 2017-8-17 10:01:19 | 显示全部楼层
有很多流程可以借鉴和学习,mark
感谢群主~
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发表于 2017-12-14 16:40:10 | 显示全部楼层
初学,跟着一起HIGH
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