Today, host- and environment-associated microbial communities like those living in the human gut, skin, soil, and water are more and more studied in terms of their functional capacity and activity. For the latter, metatranscriptomics is the method for profiling active microbial functions. BaseClear developed an industry leading hybrid metatranscriptomics workflow that combines the best alignment- and an assembly-based methods for metatranscriptomics projects. Our services provide the user with the most complete picture of the microbial functions and their expression levels in the sample.

Metatranscriptome data analysis: the next level

Our industry leading metatranscriptomics pipeline is a hybrid solution that combines the best of two worlds: an alignment- and an assembly-based method are incorporated into a novel, comprehensive, and generalizable pipeline. First, the reads are quality checked and aligned to nucleotide and protein databases of coding sequences. Those reads that did not align to the databases are assembled into transcripts, which are used to predict and annotate microbial genes. These annotated genes are then used to profile microbial functions using KEGG and COG databases. The functional expression results from the alignment- and assembly-based steps are combined into tables that provide the user with a complete picture of the microbial functions and their expression levels in the sample. The main deliverables are:

  • De novo metatranscriptome assembly (FASTA format)
  • Predicted genes and their protein translations (in FASTA and GFF formats)
  • Functional annotations of the predicted genes
  • Tables that contain microbial functions and their raw and normalised expression values for
    • KEGG KOs
    • KEGG modules
    • KEGG pathways
    • COGs
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Evaluation of computational methods for metatranscriptome analysis

Like in metagenomics, metatranscriptome data can be analysed using database alignment- or assembly-based methods. Yet both approaches come with disadvantages. While database-dependent alignment-based methods leave many NGS reads uncharacterised and cannot detect novel microbial functions, assembly-based methods suffer from long runtimes, assembly errors, and difficulties in reconstructing genes with low expression.

Read more about this evaluation in our blog

Transcriptome analysis

With our RNA sequencing (transcriptomics) service you can discover and profile the entire transcriptome of your species of interest. With no probes or primers to design, our RNA-Seq method can deliver unbiased and unparalleled information about gene expression levels. BaseClear offers strand-specific RNA-seq analysis based on sequencing on the Illumina platforms, as well as full-length transcriptome analysis on the PacBio Sequel. The RNA sequencing strategy is determined in close collaboration between the customer and our Product Managers.

Why choose our RNA-seq service?

  • Years of experience in human, plant, bacterial and fungal transcriptome sequencing projects
  • Special RNA sequencing protocols for bacterial and fungal samples available
  • Guaranteed fast delivery times with our premium services
  • Strand-specific mRNA sequencing protocols
  • Our specialists can assist you with the experimental design of your RNA-seq projects


Bioinformatics options for RNA-seq service

With our RNA-seq service we offer complete bioinformatics solutions. Options include gene expression analysis and isoform detection. Our bioinformatics department has developed state-of-the-art RNA-Seq and gene expression analysis pipelines. Our standard service includes a number of quality control steps based on the overall distribution of gene expression in the samples. All comparisons and tests include a P-value analysis to ensure the statistical significance of your results. Of course, tailored strategies are also offered. Our managers are happy to discuss your project in detail, to make sure that your research questions are answered. The ultimate goal is to provide our customers with the best possible answers to their RNA sequencing analysis research questions.


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