BIOINFORMATICS

Bioinformatics is about taking the new data and combining it with databases and, via statistics, designating important parts that can be used to draw conclusions within diagnostics and research.

We can help you with everything from experimental design, the actual sequencing, data analysis, interpretation, as well as the production of publishable figures for manuscripts or presentations.

We have experience with many different data types, including NGS data from Illumina platforms, Ion Torrent platforms, as well as NanoPore, and Sanger.

At Amplexa Genetics, we have a department of trained bioinformatics employees with a broad experience in both human genetics, molecular biology, and microbiology. In addition, we have experience with a large number of types of analysis, including:

Genomics

• Single Nucleotide Polymorphism (SNP) and variant calling on both human and microbial genomes.
• Chromosome copynumber variation (CNV) calling on human genomes.
• Comparative genomics, ie. comparison of genomes at both a macroscopic level where 1000 genomes are compared, but also within e.g. Trio analyzes in which familial genomes are examined to diagnose epileptic phenotypes.
• De novo assembly of a number of organisms, including the silverfish, herring, and a number of bacteria.
• Pan genomics where a large number of genomes are compared to find genes related to traits, such as discharge of virulence factors by a group of bacteria or during antibiotic resistance.

Transcriptomics

• Examination of gene expression and comparison between cell lines and / or organisms (differential gene-expression analysis). Of course, this also includes the ability to look for regulatory RNAs.
• Differential gene expression analysis in bacteria
• Differential gene expression analysis in eucaryotes both in bulk and at a single-cell level
• Integration of multiple differing experimental data.

Epigenomics

• DNA modifications where the DNA itself is examined for specific modifications such as methylations and acetylations.
• Discovery of transcriptional regulation through assessment of chromatin structure (ATAC-seq).

Special for Bulk RNA Sequencing

Bulk RNA-seq results in vast amount of data. Our team specializes in the bioinformatic analysis of bulk RNA-seq data. We prioritize quality control (QC) and initiate the analysis in determining the intra and inter group variability.

We utilize widely recognized techniques including STAR13 and DESeq214 and to ensure the reliability, consistency, and accuracy of your results.

As mRNA makes up only a small portion of total RNA15, we to ensure that the type of RNA we're focusing on is present in sufficient amounts for analysis. This involves measuring the distribution of different RNA types in each sample.