Wrapping up the GCC2016 Datathon

[cschu]

Hi fellow Datathoneers,

Thank you very much for taking part in the second GCC Datathon. We hope you had a good experience. In order to get an overview on current and potential future Datathon activities, we would love to hear from you what you did during the Datathon. Comments and criticism are also welcome. If you could briefly summarise things you did during the Datathon (or just link the github tickets you were working on if they are already summarised) and whether you are planning to continue working on it and post this as a reply to this ticket that would be great and help us a lot.

All the best,
@frederikcoppens , @jennaj , @cschu

[ghost]

We have working ChIP-seq and RNA-seq pipelines for mammalian system. The plan is to describe pros/cons of elements of these pipes and alternative solutions.

[msauria]

Trackster exporter is functional.
#55

On Wed, Jun 29, 2016 at 12:16 PM, test567 [email protected] wrote:

We have working ChIP-seq and RNA-seq pipelines for mammalian system. The
plan is to describe pros/cons of elements of these pipes and alternative
solutions.

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[MoHeydarian]

I think we should consider a drafting a manuscript (or some resource) where we highlight these RNA-seq and chIP-seq workflows with benefits and drawbacks of the various alternative options, as Krzys suggested. In doing so, we would introduce the Galaxy workflow environment where the alternative (tool) options can be implemented to the base workflows. It would be excellent if we could make an Interactive Tour to show this.

I can't emphasize enough that this would be targeting novice, end-users who are not familiar with NGS analysis.

Interested in feedback

[yvanlebras]

Hi everyone. +1 for the @MoHeydarian proposal!

My Datathon summary:
From #28:

• RADseq technology
  • Genetic map
    Related usegalaxy.org history
  • Population genomics
    Related usegalaxy.org history.
    There is a reference genome on the history datasets so the analysis can be made through the denovo_map as the ref_map pipelines.
  • Assemble read pairs
    Related usegalaxy.org history.

From #29:

Waiting that Stacks related tools will be reinstall after enabling conda based Galaxy tools dependencies to be install on the cloud instance. If this can be made before the end og GCC, I will create workflows for RADseq data analysis using STACKS toolsuite.

Galaxy-tour:

• Adding a Galaxy-tour for Quality check after executing a workflow (as RNAseq for exemple) using MultiQC Galaxy tool. Here is the MultiQC Galaxy-tour you can also add to the cloud-based Galaxy instance.
• small update of the old version RADseq galaxy-tour

[ssander5]

Summary:
I found and compiled publicly available, annotated data sets from published work using published workflows to use as training sets. They are small, but contain many of the common data isssue for each type.

#30

[bgruening]

@ssander5 this is great!