Researchers at the University of Würzburg have constructed a powerful and modular pipeline called ANNOgesic that provides the required analyses and simplifies RNA-Seq-based bacterial and archaeal genome annotation. It is a modular, command-line tool that can integrate different types of RNA-Seq data ...
Read More »zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
The recent development of sensitive protocols allows to generate RNA-seq libraries of single cells. The throughput of such scRNA-seq protocols is rapidly increasing, enabling the profiling of tens of thousands of cells and opening exciting possibilities to analyse cellular identities. ...
Read More »Unleash the power within RNA-seq
RNA-sequencing (RNA-seq) is an essential technique for transcriptome studies, hundreds of analysis tools have been developed since it was debuted. Although recent efforts have attempted to assess the latest available tools, they have not evaluated the analysis workflows comprehensively to ...
Read More »QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1601-4 Genome-wide miRNA expression data can be used to study miRNA dysregulation comprehensively. Although many open-source tools for microRNA (miRNA)-seq data analyses are available, challenges remain in accurate miRNA quantification from large-scale miRNA-seq dataset. We implemented a pipeline called QuickMIRSeq ...
Read More »A Bioinformatics Pipeline for the Identification of CHO Cell Differential Gene Expression from RNA-Seq Data
In recent years, the publication of genome sequences for the Chinese hamster and Chinese hamster ovary (CHO) cell lines has facilitated study of these biopharmaceutical cell factories with unprecedented resolution. Our understanding of the CHO cell transcriptome, in particular, has ...
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 »PISCES – alignment free RNA-seq quantiation and QC pipeline
Matt Shirley — PISCES: alignment free RNA-seq quantiation and QC pipeline
Read More »Quick Demo of Galaxy Bioinformatics Tools – RNA-Seq Pipeline Example
BioIT Core
Read More »Subsampling is a valid approach to facilitating efficient quantification pipeline selection using RNA-seq data
RNA sequencing (RNA-seq) is a widely applied technology that for extractings gene and transcript expression from biological samples. Given numerous quantification pipelines for RNA-seq data, one fundamental challenge is to determine identify a pipeline that can produce the most accurate ...
Read More »hppRNA – a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples
RNA-Seq technology has been gradually becoming a routine approach for characterizing the properties of transcriptome in terms of organisms, cell types and conditions and consequently a big burden has been put on the facet of data analysis, which calls for ...
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