Alignment and mapping methodology influence transcript abundance estimation

[1]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[2]  Nathan C. Sheffield,et al.  Refgenie: a reference genome resource manager , 2019, bioRxiv.

[3]  Geo Pertea,et al.  Transcriptome assembly from long-read RNA-seq alignments with StringTie2 , 2019, Genome Biology.

[4]  Son K. Pham,et al.  A revisit of RSEM generative model and its EM algorithm for quantifying transcript abundances , 2018 .

[5]  Alexis Battle,et al.  False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors , 2018, F1000Research.

[6]  A. Battle,et al.  False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors. , 2018, F1000Research.

[7]  Lior Pachter,et al.  A direct comparison of genome alignment and transcriptome pseudoalignment , 2018, bioRxiv.

[8]  M. Mascher,et al.  Genomic approaches for studying crop evolution , 2018, Genome Biology.

[9]  Claus O. Wilke,et al.  Limitations of alignment-free tools in total RNA-seq quantification , 2018, BMC Genomics.

[10]  Jiandong Shi,et al.  Deep RNA Sequencing Reveals a Repertoire of Human Fibroblast Circular RNAs Associated with Cellular Responses to Herpes Simplex Virus 1 Infection , 2018, Cellular Physiology and Biochemistry.

[11]  A. Mortazavi,et al.  Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq. , 2018, Bio-protocol.

[12]  M. Kasahara,et al.  Introducing difference recurrence relations for faster semi-global alignment of long sequences , 2018, BMC Bioinformatics.

[13]  Chirag Jain,et al.  A fast adaptive algorithm for computing whole-genome homology maps , 2018, bioRxiv.

[14]  M. Hemberg,et al.  Simulation-based benchmarking of isoform quantification in single-cell RNA-seq , 2018, Genome Biology.

[15]  Fatemeh Almodaresi,et al.  A space and time-efficient index for the compacted colored de Bruijn graph , 2017, bioRxiv.

[16]  Robert Patro,et al.  Towards selective-alignment: Bridging the accuracy gap between alignment-based and alignment-free transcript quantification , 2017, bioRxiv.

[17]  Wei Wang,et al.  Fleximer: Accurate Quantification of RNA-Seq via Variable-Length k-mers , 2017, BCB.

[18]  Shanrong Zhao,et al.  Evaluation and comparison of computational tools for RNA-seq isoform quantification , 2017, BMC Genomics.

[19]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[20]  Fatemeh Almodaresi,et al.  Improved data-driven likelihood factorizations for transcript abundance estimation , 2017, Bioinform..

[21]  Alexander Lex,et al.  UpSetR: an R package for the visualization of intersecting sets and their properties , 2017, bioRxiv.

[22]  Geet Duggal,et al.  Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference , 2017, Nature Methods.

[23]  M. Šikić,et al.  Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance , 2017, Bioinformatics.

[24]  Yadong Wang,et al.  deBGA: read alignment with de Bruijn graph-based seed and extension , 2016, Bioinform..

[25]  Martin Sosic,et al.  Edlib: a C/C++ library for fast, exact sequence alignment using edit distance , 2016, bioRxiv.

[26]  Lior Pachter,et al.  Differential analysis of RNA-seq incorporating quantification uncertainty , 2016, Nature Methods.

[27]  Giuseppe Testa,et al.  RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods , 2016, Nucleic acids research.

[28]  Peng Jin,et al.  Zika Virus Infects Human Cortical Neural Progenitors and Attenuates Their Growth. , 2016, Cell stem cell.

[29]  Lior Pachter,et al.  Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.

[30]  M. Robinson,et al.  Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences , 2015, F1000Research.

[31]  Robert Patro,et al.  RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes , 2015, bioRxiv.

[32]  Mick Watson,et al.  Errors in RNA-Seq quantification affect genes of relevance to human disease , 2015, Genome Biology.

[33]  M. Zavolan,et al.  Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data , 2015, Genome Biology.

[34]  Antti Honkela,et al.  Fast and accurate approximate inference of transcript expression from RNA-seq data , 2014, Bioinform..

[35]  Alyssa C. Frazee,et al.  Polyester: Simulating RNA-Seq Datasets With Differential Transcript Expression , 2014, bioRxiv.

[36]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[37]  Matthew A. Hibbs,et al.  RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations , 2014, Genetics.

[38]  Wei Wang,et al.  RNA-Skim: a rapid method for RNA-Seq quantification at transcript level , 2014, Bioinform..

[39]  Morgan L. Maeder,et al.  Pathways disrupted in human ALS motor neurons identified through genetic correction of mutant SOD1. , 2014, Cell stem cell.

[40]  Charity W. Law,et al.  voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.

[41]  Rob Patro,et al.  Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms , 2013, Nature Biotechnology.

[42]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[43]  Antti Honkela,et al.  Identifying differentially expressed transcripts from RNA-seq data with biological variation , 2011, Bioinform..

[44]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[45]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[46]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[47]  M. Gerstein,et al.  The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing , 2008, Science.

[48]  R. Lister,et al.  Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.

[49]  Mark D. Robinson,et al.  Differential analyses for RNA-seq : transcript-level estimates improve gene-level inferences Supplementary Material , 2015 .

[50]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[51]  Robert Patro,et al.  Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads using Lightweight Algorithms , 2013, ArXiv.

[52]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..