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.
