JAGuaR: Junction Alignments to Genome for RNA-Seq Reads
Publication Date
July 25, 2014
Journal
PLOS ONE
Authors
Yaron S. Butterfield, Maayan Kreitzman, Nina Thiessen, Richard D. Corbett, et al
Volume
9
Issue
7
Pages
e102398
DOI
https://dx.plos.org/10.1371/journal.pone.0102398
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0102398
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25062255
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111418
Europe PMC
http://europepmc.org/abstract/MED/25062255
Web of Science
000339992600013
Scopus
84904917064
Mendeley
http://www.mendeley.com/research/jaguar-junction-alignments-genome-rnaseq-reads
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1610201"], "description"=>"<p>a) Number of variants in dbSNP (v137) plotted against number of variants called at various levels of depth. Depth begins on far right at 6 bp and each point represents increasing depth of 1 bp coverage. b) Overlap of known SNVs called c) Overlap of known non-synonymous SNVs called d) Overlap of SNVs called in COSMIC. All SNP calls were assessed at depth of 6. *BWA-MEM.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "Cancer genetics", "genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "software engineering", "Software tools", "mathematics", "Applied mathematics", "algorithms", "concordance", "tools"], "article_id"=>1118592, "categories"=>["Biological Sciences"], "users"=>["Yaron S. Butterfield", "Maayan Kreitzman", "Nina Thiessen", "Richard D. Corbett", "Yisu Li", "Johnson Pang", "Yussanne P. Ma", "Steven J. M. Jones", "Inanc Birol"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0102398.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SNV_concordance_between_tools_for_one_read_set_Sample_2_/1118592", "title"=>"SNV concordance between tools for one read set (Sample 2).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-25 03:11:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1610206"], "description"=>"<div><p>JAGuaR is an alignment protocol for RNA-seq reads that uses an extended reference to increase alignment sensitivity. It uses BWA to align reads to the genome and reference transcript models (including annotated exon-exon junctions) specifically allowing for the possibility of a single read spanning multiple exons. Reads aligned to the transcript models are then re-mapped on to genomic coordinates, transforming alignments that span multiple exons into large-gapped alignments on the genome. While JAGuaR does not detect novel junctions, we demonstrate how JAGuaR generates fast and accurate transcriptome alignments, which allows for both sensitive and specific SNV calling.</p></div>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "Cancer genetics", "genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "software engineering", "Software tools", "mathematics", "Applied mathematics", "algorithms", "junction", "alignments", "genome", "rna-seq"], "article_id"=>1118597, "categories"=>["Biological Sciences"], "users"=>["Yaron S. Butterfield", "Maayan Kreitzman", "Nina Thiessen", "Richard D. Corbett", "Yisu Li", "Johnson Pang", "Yussanne P. Ma", "Steven J. M. Jones", "Inanc Birol"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0102398", "stats"=>{"downloads"=>7, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_JAGuaR_Junction_Alignments_to_Genome_for_RNA_Seq_Reads_/1118597", "title"=>"JAGuaR: Junction Alignments to Genome for RNA-Seq Reads", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-25 03:11:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1610204"], "description"=>"<p>*BWA-MEM algorithm.</p><p>**BWA memory.</p><p>Comparison of execution time and memory usage. All tools were run on a node with 64 GB memory with no other applications running.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "Cancer genetics", "genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "software engineering", "Software tools", "mathematics", "Applied mathematics", "algorithms"], "article_id"=>1118595, "categories"=>["Biological Sciences"], "users"=>["Yaron S. Butterfield", "Maayan Kreitzman", "Nina Thiessen", "Richard D. Corbett", "Yisu Li", "Johnson Pang", "Yussanne P. Ma", "Steven J. M. Jones", "Inanc Birol"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0102398.t002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Execution_Time_/1118595", "title"=>"Execution Time.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-25 03:11:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1610205"], "description"=>"<p>*BWA-MEM algorithm.</p><p>Comparison of alignment statistics and SNP concordance with dbSNP (v137) between JAGuaR, GSNAP, MapSplice2 and TopHat2. SNVs were identified with a minimum total coverage of 6 reads in order to maximize the number of SNVs for comparison while maintaining a minimum dbSNP concordance of 50% for all tools. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102398#pone-0102398-g001\" target=\"_blank\">Figure 1</a> for ROC plot of Sample 2 (Figure S3 for Sample 1 and Figure S4 for Sample 3).</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "Cancer genetics", "genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "software engineering", "Software tools", "mathematics", "Applied mathematics", "algorithms", "paired", "rna-seq"], "article_id"=>1118596, "categories"=>["Biological Sciences"], "users"=>["Yaron S. Butterfield", "Maayan Kreitzman", "Nina Thiessen", "Richard D. Corbett", "Yisu Li", "Johnson Pang", "Yussanne P. Ma", "Steven J. M. Jones", "Inanc Birol"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0102398.t001", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_results_of_three_paired_end_tag_PET_RNA_seq_libraries_/1118596", "title"=>"Alignment results of three paired end tag (PET) RNA-seq libraries.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-25 03:11:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/1610202"], "description"=>"<p>*BWA-MEM algorithm.</p><p>All SNPs called at > = 6 bp depth.</p><p>Comparison of SNP calls between tools from a simulated dataset. PET synthetic reads were generated from a reference with 652,256 planted SNPs. These fastqs were aligned to hg19 (hg19+junctions with JAGuaR) and SNPs called. SNPs that were identified by from the alignment of at least one tool and which were in the list of planted SNPs, were considered as the filtered expected SNPs. The number of recovered SNPs are the number of SNPs out of the tool's total set that are seen in the expected list. All tools have a similar ratio. Calls from the MapSplice2 alignment show the highest number of SNPs that were not planted and calls from TopHat2 show the least.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Transcriptome analysis", "Genome expression analysis", "genetics", "Cancer genetics", "genomics", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "software engineering", "Software tools", "mathematics", "Applied mathematics", "algorithms"], "article_id"=>1118593, "categories"=>["Biological Sciences"], "users"=>["Yaron S. Butterfield", "Maayan Kreitzman", "Nina Thiessen", "Richard D. Corbett", "Yisu Li", "Johnson Pang", "Yussanne P. Ma", "Steven J. M. Jones", "Inanc Birol"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0102398.t003", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Simulation_/1118593", "title"=>"Simulation.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-25 03:11:56"}

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