Bioinformatics

The AGRF bioinformatics team supports all of the services offered by the AGRF, or can work with data generated externally. Our team manages a number of established pipelines which generate high quality analysis with a rapid turnaround time, as well as supporting tailor-made analyses for custom projects.  

Our Services

Next-generation sequencing

DNA-seq: whole genome sequencing, assembly with a reference, de novo assembly, structural and functional annotation, variant calling, exome sequencing with variant calling.

RNA-seq: differential expression analysis, detection of novel splice isoforms/transcripts, transcriptome assembly, miRNA, allele-specific expression

DNA/RNA-protein interactions, e.g. ChiP-seq, RIP-Seq, CLIP-seq, HITS-CLIP 

Metagenomics

Diversity profiling: 16S, 18S and ITS targets 

Methylation

Infinium HumanMethylation450 BeadChip, Agena and Pyrosequencing analysis.

Genotyping

Analysis support for all of the Illumina BeadChips for genotyping

Microarray gene expression

Differential gene expression, heatmaps, volcano plots, gene ontology and pathway analysis

Sanger sequencing

PCR re-sequencing: primer design, SNP discovery, mutation detection, multiple alignment

What will I receive?

The AGRF makes sequence data available in standard FASTQ or FASTA formats. Sequencing files from next-generation platforms are compressed (gzipped) and FASTQ format (*.fastq.gz). FASTQ format is a text-based format for storing both a biological sequence and its corresponding quality scores.  For further information on the structure of a FASTQ file see here.  Paired end sequencing generates two files, *R1.fastq.gz for mate 1, *R2.fastq.gz for mate 2.