meeting_notes

Meeting Notes

Meeting - 2017-10-20 - 9:30am

General

• We had an introductory meeting to discuss the scope of the project, our team workflow, and to generate some initial issues.
• We agreed on the general workflow as described in workflow notes
• The HackSeq organizers have asked us to try to write up a small manuscript de
• We reviewed some of the initial data sets, and some of the possible stories to start working on. These were broken down like so:

1. Import

• We agreed that converting output from disparate tools to a common format would be useful, and would make for easily separable issues
• For each input tool, we want to write a simple parser that converts the output to BEDPE format
• I have created issues for each of the initial input tools

2. Annotation

• We agreed that it would be good/useful to be able to annotate predicted fusion events (from the BEDPE files generated above), against existing fusion databases
• To that end, I have created a set of issues along the lines of 'Document Data Source', to check whether these data sources have available APIs
• I have also stubbed out an issue to research additional data sources, as necessary

3. Aggregation

• As a first pass at this, we thought that having simple scripts (either in something like Jupyter notebooks or RMarkdown documents) to provide general overview summaries of reported events would be useful.
• As a potential stretch goal, these could be implemented in the MultiQC framework
• Note that since the BEDPE fields will differ between different tools, there may need to be a 'common core', with extensions for different tools
• For aggregation of fusions between tools, we thought we'd start by looking at tools like bedtools intersect.

4. Filter/Review

• Deferred at present, depending on how things go elsewhere

5. Visualize

• Deferred at present, depending on how things go elsewhere