Comparing reference-based RNA-Seq mapping methods for non-human primate data
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Marshall Nichols | Geoffrey S Ginsburg | G. Ginsburg | J. Lucas | T. Burke | A. Benjamin | Joseph E Lucas | Ashlee M Benjamin | Thomas W Burke | M. Nichols
[1] K. Hansen,et al. CQN (Conditional Quantile Normalization) , 2015 .
[2] G. Ginsburg,et al. Comparing reference-based RNA-Seq mapping methods for non-human primate data , 2014, BMC Genomics.
[3] A. Zaas,et al. Development of a novel preclinical model of pneumococcal pneumonia in nonhuman primates. , 2014, American journal of respiratory cell and molecular biology.
[4] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[5] C. Wheat,et al. Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species , 2012, BMC Genomics.
[6] Mark Stitt,et al. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics , 2012, Nucleic Acids Res..
[7] Chris Williams,et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization , 2012, Bioinform..
[8] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[9] Oscar Flores,et al. htSeqTools: high-throughput sequencing quality control, processing and visualization in R , 2012, Bioinform..
[10] K. Hansen,et al. Removing technical variability in RNA-seq data using conditional quantile normalization , 2012, Biostatistics.
[11] Zhong Wang,et al. Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.
[12] Cole Trapnell,et al. Computational methods for transcriptome annotation and quantification using RNA-seq , 2011, Nature Methods.
[13] Martin Goodson,et al. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. , 2011, Genome research.
[14] Derek Y. Chiang,et al. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.
[15] J. Rinn,et al. Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature Biotechnology.
[16] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[17] Y. Xing,et al. Detection of splice junctions from paired-end RNA-seq data by SpliceMap , 2010, Nucleic acids research.
[18] Serban Nacu,et al. Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..
[19] Aaron R. Quinlan,et al. Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .
[20] Colin N. Dewey,et al. RNA-Seq gene expression estimation with read mapping uncertainty , 2009, Bioinform..
[21] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[22] John C. Marioni,et al. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data , 2009, Bioinform..
[23] Siu-Ming Yiu,et al. SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..
[24] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[25] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[26] Michael Brudno,et al. SHRiMP: Accurate Mapping of Short Color-space Reads , 2009, PLoS Comput. Biol..
[27] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[28] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[29] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[30] Gunnar Rätsch,et al. Optimal spliced alignments of short sequence reads , 2008, BMC Bioinformatics.
[31] Ruiqiang Li,et al. SOAP: short oligonucleotide alignment program , 2008, Bioinform..
[32] J. Ohlrogge,et al. Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing1[W][OA] , 2007, Plant Physiology.
[33] Alex E. Lash,et al. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..
[34] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[35] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[36] T. Jukes,et al. Structural and evolutionary relationships of ferredoxins. , 1968, Brookhaven symposia in biology.