Many repetitive DNA elements are transcribed at appreciable expression levels. Mapping the corresponding RNA sequencing reads back to a reference genome is notoriously difficult and error-prone task, however. This is in particular true if chemical modifications introduce systematic mismatches, while ...
Read More »SuperTranscripts – a substitute for a reference genome
Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here researchers from the Royal Children’s Hospital, Melbourne present superTranscripts, a substitute for ...
Read More »Detecting Alternatively Spliced Transcript Isoforms from Single-Molecule Long-Read Sequences without a Reference Genome
Alternative splicing (AS) is a major source of transcript and proteome diversity, but examining AS in species without well-annotated reference genomes remains difficult. Research on both human and mouse has demonstrated the advantages of using Iso-Seq™ data for isoform-level transcriptome ...
Read More »SNP calling from RNA-seq data without a reference genome
SNPs (Single Nucleotide Polymorphisms) are genetic markers whose precise identification is a prerequisite for association studies. Methods to identify them are currently well developed for model species, but rely on the availability of a (good) reference genome, and therefore cannot ...
Read More »iPEA – de novo construction of a Gene-space based from RNA-Seq and DNA-seq data with limited computing resources
The continuing increase in size and quality of the “short reads” raw data is a significant help for the quality of the assembly obtained through various bioinformatics tools. However, building a reference genome sequence for most plant species remains a ...
Read More »Identify, quantify and annotate SNPs without any reference genome, using RNA-seq data only
SNPs (Single Nucleotide Polymorphisms) are genetic markers whose precise identification is a prerequisite for association studies. Methods to identify them are currently well developed for model species, but rely on the availability of a (good) reference genome, and therefore cannot ...
Read More »LEMONS – A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes
RNA-seq is becoming a preferred tool for genomics studies of model and non-model organisms. However, DNA-based analysis of organisms lacking sequenced genomes cannot rely on RNA-seq data alone to isolate most genes of interest, as DNA codes both exons and ...
Read More »Quantitative analysis of bacterial transcriptomes with RNA-seq
RNA sequencing has emerged as the premier approach to study bacterial transcriptomes. While the earliest published studies analyzed the data qualitatively, the data are readily digitized and lend themselves to quantitative analysis. High-resolution RNA sequence (RNA-seq) data allows transcriptional features ...
Read More »High powered processor has enabled RNA-seq data analysis more than 60 fold faster than a 16-core CPU
from UT San Diego By Bradley J. Fikes A super-fast genome processor called the Dragen Bio-IT Processor is now on sale by San Diego’s Edico Genome. The processor, which is sold on a standard PCIe computer board, is meant to ...
Read More »A Comparison of Next Generation Sequencing Technologies for Transcriptome Assembly
De novo assembled transcriptomes, in combination with RNA-Seq, are powerful tools to explore gene sequence and expression level in organisms without reference genomes. Investigators must first choose which high throughput sequencing platforms will provide data most suitable for their experimental ...
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