[PDF] Top 20 Bridger: a new framework for de novo transcriptome assembly using RNA seq data
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Bridger: a new framework for de novo transcriptome assembly using RNA seq data
... contracted de Bruijn graph even though there is a kind of correspondence between ...contracted de Bruijn graph, a splicing junction corresponds to a node, the same as an exon does (Additional file 1: Figure ... See full document
10
Clustering of Short Read Sequences for de novo Transcriptome Assembly
... (RNA-seq) using next generation sequencing technologies provides a huge amount of transcriptome data which requires an efficient and accurate method for ...assembling ... See full document
10
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
... the de Bruijn ...for de novo transcriptome evaluation, namely Rsem-Eval [4] and TransRate [5], for the specific task of identifying chi- meric transcripts in both real and simulated ...by ... See full document
19
Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape
... in RNA- Seq ...determined using nor- malised random intergenic ...Cufflinks assembly and curation is pre- sented as an annotation track ... See full document
17
Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
... methods using three RNA-seq datasets: chicken male and female embryonic tissue [24], human primary lung fibroblasts, with and without a small inter- fering RNA (siRNA) knock down of HOXA1 ... See full document
14
Transcriptome assembly from long read RNA seq alignments with StringTie2
... to transcriptome assembly: de novo and ...reference-guided. De novo transcriptome assemblers such as Trinity [5] and Oases [6] find overlaps be- tween reads and attempt to ... See full document
13
De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression
... [14]. RNA sequencing (RNAseq) is an excellent technique for investigating sev- eral non-model organisms, such as ticks, cost-effectively [15, ...sialome data analysis, many tick salivary gland ... See full document
16
Structural variant calling: the long and the short of it
... Strand- Seq have also been developed to improve the quality of as- semblies and/or SV ...ease de novo genome assembly and ...pose new methodological chal- ...apparent RNA ... See full document
14
De novo transcriptome assembly and analysis of Sf21 cells using illumina paired end sequencing
... the transcriptome was as- sembled de novo and the reads not mapped to the reference genome because the projects have been con- ducted in ...be de- tected in the transcriptome? 2) How ... See full document
7
De novo assembly of bacterial transcriptomes from RNA seq data
... measure similar to RPKM (reads per kilobase per million), which sums the number of reads for a transcript and divides by the transcript’s length and a normalization factor [7]. While the total number of reads in the sam- ... See full document
10
Exploiting orthology and de novo transcriptome assembly to refine target sequence information
... to de novo as- semblies from three tissue-specific transcriptomes (brain, liver and kidney) of these ...available data (mouse, rat, dog, pig and human) as well as newly generated paired-end ... See full document
12
Comparative studies of Toxoplasma gondii transcriptomes: insights into stage conversion based on gene expression profiling and alternative splicing
... high-throughput RNA-sequencing data to assemble transcripts using genome-based and de novo ...Trinity-based de novo and genome-based strategies, and found that the ... See full document
11
A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly
... throughput RNA sequenc- ing (RNA-Seq) ...the data analysis ...Current RNA-Seq applications involve assembly of the transcriptome, with or without the refer- ence ... See full document
10
A consensus approach to vertebrate de novo transcriptome assembly from RNA seq data: assembly of the duck (Anas platyrhynchos) transcriptome
... available, de novo transcriptome assembly enables a cost effective insight into the identification of tissue specific or differentially expressed genes and variation of the coding part of the ... See full document
6
Evaluation of de novo transcriptome assemblies from RNA Seq data
... tome assembly evaluation by presenting the DETONATE methodology (DE novo TranscriptOme rNa-seq Assem- bly with or without the Truth Evaluation) and software ...an assembly ... See full document
21
Detecting Staphylococcus aureus Virulence and Resistance Genes: a Comparison of Whole Genome Sequencing and DNA Microarray Technology
... the de novo assembled ...of de novo assembly (target was identified in reference-mapped ge- nome), (ii) insufficient genome coverage during shotgun se- quencing (target was identified ... See full document
9
Fast skeletal muscle transcriptome of the Gilthead sea bream (Sparus aurata) determined by next generation sequencing
... approximation using the translated ...loaded using BioMart tool from ESEMBL ...performed using Inparanoid 4.0 [65]. Comparisons were performed using the gilthead sea bream translated ... See full document
17
A new algorithm for de novo genome assembly
... of de novo genome assembly. Some of the de novo genome assemblers ...a de Bruijn graph approach. Currently, the approaches based on the de Bruijn graph are the most ... See full document
140
De novo assembly of a genome-wide transcriptome map of Vicia faba (L.) for transfer cell research
... strategy using Illumina sequencing was successful in generating 21,297 contigs, of which ...that de novo assem- bly of 20,881 contigs from Dahlia may represent about half the gene loci in this ... See full document
9
Genome-Wide Analysis of RNA Secondary Structure in Eukaryotes
... rRNA-depleted RNA samples were treated with a double- strand specific ribonuclease per manufacturer’s instructions (RNase V1, Applied Biosystems (Foster City, ...purified using a phenol:chloroform ...PNK, ... See full document
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