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C3G offers a wide range of standardized and tailored analysis services to researchers, who in turn benefit from our extensive experience analyzing data from various sequencing applications with state of the art computation methods.
In this application, C3G will quantify transcripts and genes using a reference genome and test for differential expression across experimental conditions. It is also possible to call single nucleotide variants (SNVs), detect fusion gene events and assess alternative splicing events.
rRNA amplicon-seq metagenomics
The C3G can process your Illumina, PacBio pyrotags amplicons from the 16S, 18S or ITS amplicons. OTUs are picked and diversity is analyzed within and between communities. Further analyses include differential abundance testing or metagenome functional content prediction.
RNA-seq de novo
This analysis assembles reads to transcripts in the absence of a reference genome, annotates transcripts and tests for differential expression. This is well suited to uncharacterized organisms.
Hybrid assembly of large genomes
The C3G can perform de novo assemblies of genomes using Illumina paired-end reads, possibly supplemented with long insert mate-pairs and lower coverage PacBio long reads to scaffold contigs and fill gaps.
C3G’s standard miRNA analysis quantifies know miRNAs, discovers novel ones using a reference genome and performs differential expression analysis. Additional analysis may include pathway testing, target candidates analysis or miRNA editing.
C3G offers state of the art DNA-seq analyses detects and annotates variants in whole exomes, whole genomes or high coverage amplicons. The analysis can also be pushed further by assisting with variant prioritization, or perform advanced cancer related analysis.
PacBio genome assembly
C3G offers to assemble small bacterial to larger genomes sequenced with the Pacific Biosciences technology. Genomes can be polished with Illumina short reads, circularized, called for base modifications and annotated.
Our team analyzes DNA fragments from immunoprecipitated chromatin by calling alignment peaks on the genome, annotating the said peaks and performing additional analyses such as motif enrichment and discovery. Designed experiments can be analyzed by testing for differential binding between experimental conditions.
Our team offers to analyze data coming from bisulfite converted DNA assayed by various sequencing assays such as RRBS, CpG capture, whole genome sequencing or microarrays. Our analysis computes methylation levels and performs differential analysis between experimental conditions.
C3G’s standard analysis will QC, preprocess and perform differential expression analysis on expression array data. This is usually followed by pathway analysis and the preparation of custom visualizations.
C3G offers Hi-C data analysis and provides interaction matrices at several resolutions, compartment analysis, topologically associating domain (TAD) predictions, as well as significant chromosomal interactions. Further analyses may include comparisons across samples/conditions and integration of various sample data (expression data, methylation, CTCF/histone binding sites…) with Hi-C data.
- Single-cell RNA sequencing
- Single-nucleus ATAC-seq
- CRISPR-Cas9 processing and statistical analysis
- GBS, RAD-Seq
- Whole metagenome/metatranscriptome analysis