Our core sequencing service has two Illumina HiSeqs and a MiSeq. The FAS Informatics group is committed to providing a fast basecalling and QC service for all users of the facility. Beyond this we strongly encourage people to get in contact with us and we’ll be happy to discuss things further. We aim to work alongside researchers with the intention of spreading knowledge and enabling people to run analyses themselves. As we grow we are building workflows and pipelines to enable more people to be self sufficient in bioinformatics analysis.

Support

In summary we provide:

  • Advice on sequencing needs (length, type and number of reads, recommendations for replicates).
  • Basecalling and demultiplexing of core sequencing runs.  This includes checking the base yield and quality and working to extract data from the remaining reads.
  • Quality control statistics of reads.
  • Advice on which tools are suitable for further analysis.

Other bioinformatics support:

  • Basic unix command help and navigating the cluster
  • How to submit jobs to the queueing system.
  • De novo assembly of transcriptome data.
  • Transcriptome construction both with and without a reference genome.
  • Calculation of expression and differential expression from constructed transcripts.
  • Alignment of related genomes (close and more distant)
  • SNP calling using tools such as GATK/samtools
  • ChIP-Seq analysis mainly using MACS
  • Visualization of NGS data (IGV browser/Tablet  browser/uploading features to UCSC/Ensembl)
  • Annotation of  genes (blast/interpro/pfam/GO)
  • Custom script/algorithm writing.   We have limited resources (although much enthusiasm) for this.   Due to resource limitations at the  moment we try to limit this to areas where we are sure the tools built can benefit multiple groups.
  • Basic R usage and using bioconductor packages for sequence analysis
  • Phylogenetic reontstruction of trees using tools such as phylip, mrbayes, raxml (also GUIs like mega, geneious)
  • Using blast to search common databases.  Constructing custom blast databases.
  • Searching protein domain databases using interproscan.

LIMS Procedures