Data Analysis

miRNAs play a key role in normal physiology and various diseases. miRNA profiling through next generation sequencing (miRNA-seq) has become the main platform for biological research and biomarker discovery. However, analyzing miRNA sequencing data is challenging as it needs significant ...

This article originally appeared on Getting Genetics Done and graciously shared here by the author Stephen Turner. I’ve been asked a few times how to make a so-called volcano plot from gene expression results. A volcano plot typically plots some ...

Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes ...

BigWig, a format to represent read density data, is one of the most popular data types. They can represent the peak intensity in ChIP-seq, the transcript expression in RNA-seq, the copy number variation in whole genome sequencing, etc. UCSC Encode ...

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in ...

Genetic variation in cis-regulatory elements is an important cause of variation in gene expression. Cis-regulatory variation can be detected by using high-throughput RNA sequencing (RNA-seq) to identify differences in the expression of the two alleles of a gene. This requires ...

RNA-seq gene profiling – a systematic empirical comparison Nuno A Fonseca, John A Marioni, Alvis Brazma Accurately quantifying gene expression levels is a key goal of experiments using RNA-sequencing to assay the transcriptome. This typically requires aligning the short reads ...

Making sense of childhood growth  Background Dr Adam Stevens, is a human development systems biologist working in Professor Peter Clayton’s group at the UK’s University of Manchester. In addition to industrially-funded and commercially-sensitive research into drug responses, Dr. Stevens and ...

RNA-seq techniques generate massive amounts of expression data. Several pipelines (e.g. Tophat and Cufflinks) are broadly applied to analyse these data sets. However, accessing and handling the analytical output remains challenging for non-experts. Researchers at the Helmholtz Center Munich now ...

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. ...