On 28 January, the Genomics Research Platform team, led by Dr Alka Saxena, held their Third Annual Partek Next Generation Sequencing workshop. Ulrich Kadolsky, a Senior Bioinformatician, who organised the Workshop along with Hollie Bolt, shares his experience of the day.
Analysing sequencing data has a steep learning curve – researchers need both computer competence and a strong biology background. Partek Flow is a web-based software where no knowledge of the command line or scripting is needed to start bioinformatics analyses. We have been holding these workshops for a few years now to introduce researchers to the resource and encourage them to get their hands dirty analysing Next Generation Sequencing datasets.
The workshop started with a gentle introduction to Partek Flow by Ivan Lukic, Senior Field Application Scientist from Partek. Ivan gave a live demonstration of how sequencing data could be processed and analysed. Along with myself, we covered common analysis techniques and topics: from variant finding in DNA, to differential gene expression between samples in RNA-Seq data. Several researchers had expressed an interest in learning how to analyse data from ChIP- and ATAC-Seq data, so Ivan showed us the versatility of Flow in handling different types of NGS data.
The Genomics Research Platform recently acquired a 10X Genomics Chromium Controller, a single cell capture solution which can be used to identify new cell types. In the afternoon, Shichina Kannambath, a Senior Bioinformatician in the Platform, took us through analysing data from Chromium libraries and Partek Flow’s cell clustering and visualisation tools.
The centrepiece of the day was the data analysis workshop, when the attendees and worked through Partek Flow tutorials by themselves. Here they put theory into practice and (we hope!) built confidence using the tools and analysing their NGS data. For me, it’s always a pleasure to help de-mystify the complicated subject of bioinformatics and make it more accessible. From the insightful questions which participants asked and how quiet the room was as people worked their way through the tutorials, I think everyone learnt a lot and enjoyed putting their new skills to use.
On Tuesday morning we held a ‘Bioinformatics Clinic’ – 1:1 sessions for researchers to ask a bioinformatician questions about their own project. This was a great opportunity to go into more detail and help them propel their analysis forward.
Attendee Olga Mikhaylichenko said: “I got a great overview of Partek’s utilities and enjoyed the hands-on experience. Can’t wait to try it out on my data!”
Attendee Radhika Kataria said: “The course gave a great overview into how to easily process RNA and DNA sequencing data using the Partek Flow platform, this included looking at features in DNA such as single nucleotide and structural variations this was particularly useful to me as I work with transcriptomic and genomic data from cancer patients.”
I hope the attendees will feel more confident about Next Generation Sequencing data and to see many of the participants using it for their analysis in the near future – from cells to results!