Analysis Pipelines

Choosing a next-generation sequencing pipeline

rna-seq

The next-generation sequencing (NGS) technologies are revolutionary tools which have made possible achieving remarkable advances in genetics since the beginning of the twenty-first century. Thanks to the possibility to produce large amount of sequence data, these tools are going to ...

Read More »

piPipes – a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

PIWI-interacting RNAs (piRNAs), 23-36 nt small silencing RNAs, repress transposon expression in the metazoan germ line, thereby protecting the genome. Although high-throughput sequencing has made it possible to examine the genome and transcriptome at unprecedented resolution, extracting useful information from ...

Read More »

BioVLAB-MMIA-NGS – MicroRNA-mRNA Integrated Analysis using High Throughput Sequencing Data

rna-seq

It is now well established that microRNAs (miRNAs) play a critical role in regulating gene expression in a sequence specific manner and genome-wide efforts are underway to predict known and novel miRNA targets. However, the integrated miRNA-mRNA analysis remains a ...

Read More »

RNA-Seq with iReport and InSilico DB

rna-seq

RNA-Seq, or transcriptome sequencing, continues to be an exciting way to explore gene expression using next-generation sequencing (NGS). But for many researchers, the interpretation of RNA-Seq data remains a daunting task because they are using spreadsheets to read transcript names ...

Read More »

SUPPA – a super-fast pipeline for alternative splicing analysis from RNA-Seq

rna-seq

High-throughput RNA sequencing allows genome-wide analyses of pre-mRNA splicing across multiple conditions. However, the increasing number of available datasets represents a major challenge in terms of time and storage required for analyses. Now, a team led by researchers at the ...

Read More »

Comparison of Computational Methods for Identification of Allele-Specific Expression based on Next Generation Sequencing Data

rna-seq

Allele-specific expression (ASE) studies have wide-ranging implications for genome biology and medicine. Whole transcriptome RNA sequencing (RNA-Seq) has emerged as a genome-wide tool for identifying ASE, but suffers from mapping bias favoring reference alleles. Two categories of methods are adopted ...

Read More »

OncoRep: An n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing

rna-seq

Breast cancer comprises multiple tumor entities associated with different biological features and clinical behaviors, making individualized medicine a powerful tool to bring the right drug to the right patient. Next generation sequencing of RNA (RNA-Seq) is a suitable method to ...

Read More »

Omics Pipe – A Computational Framework for Reproducible Multi-Omics Data Analysis

rna-seq

Omics Pipe is a computational framework for reproducible multi-omics data analysis that supports several next generation sequencing best practice pipelines, such as RNA-seq, miRNA-seq, Exome-seq, whole genome-seq and ChIP-seq. The purpose of Omics Pipe is to provide researchers with an ...

Read More »