Mosquito Informatics (INFRAVEC)
Day 1 consists of introductions and summary talks with a guest lecture about the use of high-throughput genomic data sets in vector biology and then a walk through with exercises explaining programmatic access to VectorBase data using the Ensembl Application Programming Interface (API). Finally participants will initiate alignment of NGS dataset to a reference genome within the Galaxy platform
Day 2 explores builds on the aligned NGS data from Day 1 including the visualisation of the alignments and some simple analyses to get FPKM expression values for genes (to identify differential expression) and looking at calling variations (SNP detection). The session will end with discussion on how to improve data at VectorBase (community annotation efforts) and outreach activities (where to get help, what to expect from INFRAVEC/VectorBase).
Target audience: Researchers and research teams, including PhD students and postdocs. Participants will need to have experience of the Perl scripting language and a minimum of one year’s experience in the field of bioinformatics is preferable but not mandatory.
Prerequisites: The workshop is organised by the INFRAVEC Project as part of its Transnational Access activities aimed at providing funding to all researchers. Eligibility criteria for the provision of funding in the form of units of access are set by the EU Commission.
|Day 1 - 5 February 2014|
|13:00-13:15||Workshop Introduction, information for participants||Dan Lawson|
|13:15-14:00||Introduction to INFAVEC & VectorBase||Dan Lawson|
|14:00-15:00||Introductory concepts - Overview of basic concepts (Genome sequencing/assembly, annotation & HTG data sets)||Dan Lawson|
|15:30-16:30||Lecture on use of Galaxy||Bob MacCallum/ Dan Lawson|
|16:30-17:30||Sequence alignments of reference genomes
Alignment of RNAseq transcriptome or genomic re-sequencing data to reference genomes. Participants are encouraged to use their own data for this exercise. Set up alignments at Pathogen Portal or VectorBase Galaxy sites
|19.30||Evening meal at the Hinxton Red Lion|
|Day 2 - 6 February 2014|
|09:00-09:15||Review progress on NGS alignments from previous day||Dan Lawson|
RNAseq analysis. Analysis of aligned transcriptome data, FPKM expression values, visualisation in VectorBase
|10:30 - 11:00||Tea/coffee break|
|11:00 - 12:30||
Programmatic access to VectorBase data. Walkthrough & hands on exercises for programmatic access to datasets including BioMart queries, Perl API
|12:30 - 13:30||Lunch|
|13:30 - 15:00||
Genomic re-sequencingAnalysis of aligned genomic data, SNP calling, SNP consequences, visualisation in VectorBase
|15:00 - 15:30||Tea/coffee break|
|15:30 - 16:30||Free time to work on participants datasets|
|16:30 - 17:00||
Submission of data and Community outreach efforts. Getting help (both offline and interactive), examples of interactions with VectorBase/INFRAVEC staff
|17:00 - 17:30||Wrap up session and questions||Dan Lawson|
Notes: The workshop does not require you to bring your own computer. Course material is provided. Participants are encouraged to bring their own data and discuss any technical issues during the dedicated practical sessions of the workshop. The teaching language will be English.
The training workshop will take place at the EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK (approx. 10 miles south of the city of Cambridge).