RNA-seq data, transcriptome assembly and annotation
Bridger: a new framework for de novo transcriptome assembly using RNA seq data
... novo transcriptome assembly by introducing an auxiliary graph, without the help of any genomic in- ...real data, Bridger shows best sensitivity and accuracy among all de novo assemblers, and even ...
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Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data
... pig transcriptome [ 28 ] used Pac- Bio Iso-seq data from 38 porcine tissues to improve the previous pig genome assembly ...mina RNA sequencing (RNA-seq) data from ...
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Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria× ananassa)
... a transcriptome when a reference genome is available: reference-based, de novo, or a combination of the two 18 ...gene annotation is incomplete. De novo assembly of a complex transcriptome ...
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A consensus approach to vertebrate de novo transcriptome assembly from RNA seq data: assembly of the duck (Anas platyrhynchos) transcriptome
... of data enables a robust assembly to be produced by multiple methods without the need for very high memory ...of assembly obtained. For this dataset the use of MK in the assembly generated a ...
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Transcriptome Assembly, Gene Annotation and Tissue Gene Expression Atlas of the Rainbow Trout
... by transcriptome information that will enhance genome assembly and ...Previously, transcriptome reference sequences were reported using data from different ...well-annotated ...
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Improved Annotation with de novo Transcriptome Assembly in Four Social Amoeba Species
... Improved Annotation of 3 ' Untranslated Regions and Complex Loci by 633 Combination of Strand-Specific Direct RNA Sequencing, RNA-Seq and ...
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Transcriptome assembly from long read RNA seq alignments with StringTie2
... guide annotation, we ran StringTie2 and FLAIR on the human chromosome 19 ONT data using random samples of the chromosome 19 annotation, which we varied to contain from 1 to 100% of the ...of ...
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Evaluation of de novo transcriptome assemblies from RNA Seq data
... of transcriptome and genome ...genome assembly it is generally assumed that all chromosomes are sequenced to the same sequenc- ing depth, whereas with transcriptome assembly one has to ...
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Computational Pipeline for Human Transcriptome Quantification Using RNA-seq Data
... coverage. This visualization need is addressed by another key feature of SAMMate. SAMMate can take the alignment results stored in SAM files and export the genome information to wiggle (.wig) files where the wiggle ...
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Novel methods in transcriptome analysis using RNA-seq
... of RNA-seq data and short length of RNA-seq reads have imposed unprecedented computational ...in RNA-seq data, in order to get better understanding of ...
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De novo assembly of bacterial transcriptomes from RNA seq data
... DNA-seq data and 12 sets of RNA-seq data corresponding to a range of ...quality transcriptome assemblies and outperformed other leading ...novo transcriptome ...
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Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
... simulated RNA-seq data, we showed that it improves significantly the sensitivity of the previous ver- sion of KisSplice, while also improving its ...input data contains high pre- mRNA content ...
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Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
... simulated RNA-seq data, we showed that it improves significantly the sensitivity of the previous ver- sion of KisSplice, while also improving its ...input data contains high pre- mRNA content ...
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Optimizing de novo assembly of short-read RNA-seq data for phylogenomics
... bp RNA-seq reads using Oases, Trinity, Trans-ABySS and SOAPdenovo-Trans to transcripts from genome annotation of the model plant Ricinus ...minimizing assembly chimeras and ...seven ...
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RNA-seq data analysis pipeline
... typical RNA-seq data analysis pipeline because it is well-documented, often updated and improved and has a wide selection of ...transcript annotation file, TopHat2 aligns the reads only to the ...
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Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation
... of RNA levels from RNA-seq data. RNA-seq data produce digital counts of transcript abundance, allowing to quantify transcript levels in a straightforward ...used ...
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A RNA-seq analysis to describe the boar sperm transcriptome and its seasonal changes
... analyzed RNA-seq data from 9,795 human experiments from the GTEx project and concluded that the human genome annotation incorporates most of the Homo sapiens genes but still lacks a large ...
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Computational analysis of bacterial RNA-Seq data
... priori annotation bias sug- gestive of ...our RNA-seq data, and we found evidence of co-transcription for all six pairs of genes (Figure ...our RNA-seq data, and we found ...
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A Novel Assembly Algorithm That Optimizes For RNA-Seq Data
... of data. For ERCC data, all assemblers gave acceptable ...graph-based assembly methods would not generate many incorrect ...real data illustrate, the de Bruijn graph-based assembly ...
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IsoTree: A New Framework for De novo Transcriptome Assembly from RNA-seq Reads
... Since the computation is carried on one splicing graph after another, and the size of the splicing graph differs not much for different gene, Isotree is scalable for most simulated and real data. In addition, the ...
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