[PDF] Top 20 Evaluation of de novo transcriptome assemblies from RNA Seq data
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Evaluation of de novo transcriptome assemblies from RNA Seq data
... axolotl RNA-Seq time ...additional DE UP oncogenes (FOSL1 and JUNB) that are not identified using the published assembly ...being DE UP during the mid- dle phase (3 to 14 days) of the time ... See full document
21
Innovative Algorithms and Evaluation Methods for Biological Motif Finding
... human RNA-Seq data. The human genome data (hg19, NCBI build 36) was downloaded from UCSC [51] and CCDS [52], together with the coordinates of the transcripts in the KnownGenes ... See full document
105
Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
... 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 [25], and yeast grown ... See full document
14
De novo assembly of bacterial transcriptomes from RNA seq data
... the assemblies produced by Rockhopper 2, Trinity, and SOAPdenovo2 across the 12 RNA-seq data sets and the results are provided in Figure 3 and Additional file ...chaea data sets, but ... See full document
10
Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape
... result from the incom- plete annotation of single longer genes or extended multi- exonic transcripts, we merged those transcripts present within a 2-kbp genomic interval of a 3′ end (after having tested multiple ... See full document
17
A consensus approach to vertebrate de novo transcriptome assembly from RNA seq data: assembly of the duck (Anas platyrhynchos) transcriptome
... metrics from the different tools varied, for example CLC was quicker but generated contigs with a lower N50 ...SK assemblies, Oases produced the ones with the highest number of bps, mean transcript lengths, ... See full document
6
Metassembler: merging and optimizing de novo genome assemblies
... different de novo gen- ome assembly algorithms can vary greatly on the same dataset, although it has been repeatedly demonstrated that no single assembler is optimal in every possible quality metric [6 – ... See full document
10
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
... sensitivity from the 5 to the 15% pre-mRNA data- ...the data. Trinity, on the other hand, dropped significantly from 98 to ...slightly from 95 to 91%, and Oases dropped moderately, ... See full document
19
Bridger: a new framework for de novo transcriptome assembly using RNA seq data
... de novo assembler that outperforms Trinity in both sensi- tivity and ...all data, while Bridger allows using different user-specified k values for different data; (2) Bridger uses a rigorous ... See full document
10
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 chain ... See full document
13
Transcriptome signatures associated with meningioma progression
... (both de novo and secondary) and grade III meningi- omas, which had a smaller fusion burden (one-way ANOVA with Tukey’s multiple comparison test; Grade I NP ...vs. de novo Grade II, p = ... See full document
13
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes
... and de novo assembled tran- scriptome into a compact superTranscriptome using chicken RNA-seq data, to allow identification of novel transcribed ... See full document
10
Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies.
... as RNA-Seq [4], has the advan- tage that sequence characterisation is focused on functionally important regions of the ...on transcriptome characterisation in non- model organisms remain rather ... See full document
8
Analysis of the Aspergillus nidulans transcriptome using high-throughput RNA sequencing
... to RNA-seq reads, indicating broad transcriptional utilisation of the ...findings from previous sequencing studies. These data also indicate a significant level of antisense transcription, ... See full document
264
<p>Construction and Analysis of a Long Non-Coding RNA-Associated Competing Endogenous RNA Network Identified Potential Prognostic Biomarkers in Luminal Breast Cancer</p>
... The RNA-seq data and miRNA-seq data of luminal A breast cancer in the The Cancer Genome Atlas (TCGA) database were downloaded and compared with those in the miRcode database to obtain ... See full document
12
De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq
... before de novo assembly was carried out using CLC Genomics ...for data trimming are: Quality trim limit = ...trimmed data were also removed using CLC Genomics Workbench and the seven trimmed ... See full document
17
The evolution of combined molecular targeted therapies to advance the therapeutic efficacy in melanoma: a highlight of vemurafenib and cobimetinib
... samples from five patients with acquired resistance to combined dabrafenib and tram- etinib therapy demonstrated that some of the MAPK pathway mutations that arise in the setting of monotherapy such as MEK1/2 ... See full document
14
Genome-wide profiling of RNA editing sites in sheep
... and RNA-seq data to detect 18,644 and 25,407 RDDs in sheep kidney and spleen, however, most of the detected RDDs were ...modest RNA-seq coverage, high quality of mapped reads and high ... See full document
9
De novo likelihood based measures for comparing genome assemblies
... sampled from the genome (with the exception of the dependence imposed by mate-pair exper- ...sequencing data as new instruments and/or chemistries become avail- ... See full document
18
De Novo Initiation of RNA Synthesis by the RNA-Dependent RNA Polymerase (NS5B) of Hepatitis C Virus
... Therefore, we also examined if the C-terminal 18 amino acids of NS5B have any effects on in vitro RdRp activity under the conditions used in this study. A full-length NS5B, designated 1b-42F, was restored, expressed, and ... See full document
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