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scRNA-seq Differential Expression with EdgeR

Why Differential Expression Analysis with Single-cell RNA-seq data? The differential expression (DE) analysis has been used in bulk RNA-seq analysis for many years. It statistically measures changes in gene expression levels between different groups. With bulk RNA-seq analysis many cells are sequenced at the same time, so gene expression levels are commonly measured at the tissue level. Thus, the differences

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Long read LongQC

Quality Assessment with LongQC

Specific tools for a new generation of sequencing Third Generation Sequencing (TGS) is getting a notable increase in relevance by surpassing some of the limitations of NGS technologies. In that sense, the main feature of TGS is the capacity to produce much longer reads than NGS. These long reads facilitate the assembly of complex genomes and the study of alternative

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Monocle3 in OmicsBox: scRNA Seq trajectory interference

What is Monocle 3? Monocle 3 is a scRNA-Seq data analysis toolkit developed by Trapnell lab. It is written in R and introduced the notion of pseudotime. Monocle 3 can help perform three major types of scRNA-data analysis: Clustering & classification of cells by putative cell types Assignment of pseudotime to cells and, in turn, construction of single-cell trajectories to

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Long Read Transcriptome with SQANTI3

Transcriptome Analysis with SQANTI3

Transcriptome analysis is a challenging bioinformatic problem. In eukaryotic transcriptomes, alternative splicing and alternative polyadenylation are the most complex issues. Genome-wide analysis of alternative splicing has been studied with short-read RNA sequencing for a while. Nevertheless, this technology needs a subsequent assembly, which is difficult to be resolved in ambiguities in complex loci.

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Biobam receives a grant from the Valencian Innovation Agency – AVI

  We are proud to announce that we have received a grant from the Valencian Innovation Agency – AVI Our I+D+i project “EVOLUTION OF THE COMPANY’S CLOUD SYSTEM TOWARDS AN ADVANCED ELASTIC PLATFORM FOR HIGH-PERFORMANCE COMPUTING AND MASSIVE SEQUENCING DATA PROCESSING” has received a grant from the Valencian Innovation Agency (AVI) in the line L3 Industrial Doctorate (innodocto) to support

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metatranscriptomics SortMeRNA OmicsBox rRNA ribosomal removal filtering

rRNA Removal with SortMeRNA in OmicsBox

Introduction RNA-seq data from metatranscriptomics NGS projects contains both coding and non-coding types of RNAs. Before any gene expression or taxonomic analysis, it is important to separate reads in families of messenger RNAs and ribosomal RNAs (rRNAs). SortMeRNA, first released in 2012, is a fast and accurate tool for filtering ribosomal RNAs in metatranscriptomics datasets. The core algorithm is based

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