BSAseq parameters, source?

[nikostr]

Hey! First off: thank you for an excellent paper! Really nice seeing this written up, and definitely something that will be useful to me and others.

In the paper, supplementary materials and online documentation I haven't managed to find the exact parameters/scripts used to run the steps of the pipeline, beyond the GUI provided by SciApps. Are these available somewhere? Will the source of the Shiny app be made available?

Once again, thank you!

[liyawang]

Thanks for asking. Here is a detailed tutorial for running BSAseq: https://learning.cyverse.org/projects/sciapps_guide/en/latest/bsa.html

And you can load the example data from this workflow: https://www.sciapps.org/wf_id/8

The second link has all parameters preset. Generally, you only need to use the default parameters. The Shiny app is currently embedded with the workflow and it will not work without the workflow. E.g. we pre-computed everything before launching the Shiny app.