Sequencing data
Finding the association of mRNA and miRNA using Next Generation Sequencing data of Kidney renal cell carcinoma
... Abstract MicroRNAs (miRNAs) are a class of 22-nucleotide endogenous noncod- ing RNAs, plays important role in regulating target gene expression via repress- ing translation or promoting messenger RNAs (mRNA) degradation. ...
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PeSV-Fisher: identification of somatic and non-somatic structural variants using next generation sequencing data.
... Next-generation sequencing technologies expedited research to develop efficient computational tools for the identification of structural variants (SVs) and their use to study human ...deeper data is ...
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McClintock: an integrated pipeline for detecting transposable element insertions in whole-genome shotgun sequencing data
... simulated data sets using reference TE annotations and canonical TE sequences from Carr et ...simulated sequencing data set), or (iv) within a 500-bp window either side of the ...
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Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data
... transcriptome sequencing data derived from next-generation DNA sequencing ...transcriptome data (GTF files) using gene coordinates available from the UCSC genome browser and allows the ...
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Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data.
... generation sequencing is extensively applied to catalogue somatic mutations in can- cer, in research settings and increasingly in clinical settings for molecular diagnostics, guid- ing therapy ...of ...
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Compression of FASTQ and SAM format sequencing data.
... the data was kept in the original ...Generally sequencing data is either in an unsorted FASTQ file or an aligned and hence sort-able alignment file ...deep data being the notable exception) ...
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The impact of post-alignment processing procedures on whole-exome sequencing data
... The use of post-alignment procedures has been suggested to prevent the identification of false-positives in massive DNA sequencing data. Insertions and deletions are most likely to be misinterpreted by ...
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VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data.
... by sequencing technologies; and (iii) work on WGS, RNA-Seq or targeted sequencing ...NGS data with a specified virus type, like VirusSeq and ViralFusionSeq, but also be applied readily to samples ...
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Ancestral alleles in the human genome based on population sequencing data.
... Ancestral allele information is useful for genetics studies. Previously, the identification of an- cestral alleles was primarily based on sequence alignments between species. Alternative ways to identify ancestral ...
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Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
... used data from the alignment of experimentally obtained rice reads (63 million Illumina paired-end reads) with the simulated rice genome containing artificial ...pooled sequencing data) does not fit ...
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An Overview of the Analysis of Next Generation Sequencing Data
... generation sequencing generates huge amounts of data, which poses a challenge both for data storage and analysis, and consequently often necessitates the use of powerful computing facilities and ...
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Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer.
... Deep sequencing technologies provide a powerful means to identify responsive genes, which creates a need for computational methods able to analyze dynamic and multi-level deep sequencing ...a ...
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Evaluation of MC1R high-throughput nucleotide sequencing data generated by the 1000 Genomes Project
... next-generation sequencing allows simultaneous processing of several genomic regions/individuals, increasing the availability and accuracy of whole-genome ...flaws, data obtained by next-generation ...
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Microsatellite characterization and marker development from massive sequencing data of the blenny Salaria pavo
... However, a major drawback of microsatellites is that for most species there is little or no sequence data. Until recently, the advantages of microsatellite markers were partially offset by the difficulty inherent ...
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Quantitative identification of mutant alleles derived from lung cancer in plasma cell-free DNA via anomaly detection using deep sequencing data.
... exome sequencing using plasma DNA from cancer patients [22], Analysis of cancer genomes at any stage of the disease course might uncover genetic changes leading to disease progression or drug ...
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Analysis of RAD sequencing data from species of Mediterranean cicadas
... meu data set e como iniciaria o tratamento com o ipyrad; comentando os meus resultados que iam aparecendo e melhorias a fazer; resolver de erros e problemas que iam surgindo, assim como todas as palavras de ...
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A bioinformatics approach for determining sample identity from different lanes of high-throughput sequencing data.
... of data influences concordance rates of called genotypes, we performed two sets of comparisons between related and unrelated lanes by titrating sequenced ...
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Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system
... All sequencing data were curated using mothur ...raw data can be obtained from the Sequence Read Archive at NCBI under accession SRP051686, which are associated with BioProject ...contain data ...
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Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data.
... CLIP data (Fig 1B). Here we considered two AGO CLIP sequencing data sets, the human HEK293 PAR-CLIP data set [2] as well as a HITS-CLIP data set in activated mouse CD4+ T cells ...two ...
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DNA extraction, PCR, and DNA sequencing
... sequence database. We observed identity values between 97% and 99% for L. sativae (Data not shown). These values confirmed that all specimens examined in this study belonged to the species L. sativae. Previously, ...
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