Bioinformatic tools and datasets

As part of our research, we have developed tools to analyse the wealth of data which is now available.

Bioinformatic tools

Microbiome amplicon analysis pipeline

Galaxy pipeline for the analysis of paired-end 16S rRNA data from Illumina Miseq (Casava >=1.8) that performs: QC and clean-up of input data, removes singletons and chimeras, builds OTU table and phylogenetic tree , performs alpha and beta diversity analysis.

Available from:
Galaxy | Tool Shed

Datasets

Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci

Capture Hi-C was carried out to characterise the interactions of confirmed susceptibility loci for four autoimmune diseases: rheumatoid arthritis (RA), type 1 diabetes (T1D), psoriatic arthritis (PsA) and juvenile idiopathic arthritis (JIA) with the aim of linking associated variants with disease-causing genes.

We have tested the interactions in two complementary experiments: the first, Region Capture, targets regions associated with disease; the second, Promoter Capture, provides independent validation through capturing all known promoters within 500kb of lead associated disease SNPs.

All experiments were performed in human T-cell (Jurkat) and B-cell (GM12878) lines in duplicate.

Release date: 24 November 2015

Available from:
GEO Accession viewer