How to interpret the output & visualize it

[leonorrib]

Dear authors,

Thank you for developing this nice tool. I would like to know how to interpret the output files of decontaminer and whether there is an option of your tool that visualizes the output of it.

Best regards,
Leonor

[amarinderthind]

Thanks for reaching out ... the collecInfo.sh script yields some HTML pages which come with visualization.

Alternatively one could also try the interactive server available here Server seems Down at the moment. On this server, you can upload the result file to visualize, and also allow you to play interactively with some thresholds.

Let me know if this helps, otherwise, I can share the R script.

Make sure you executed these three commands:
(a) decontaMiner.sh
(b) filterBlastInfo.sh and
(c) collectInfo.sh

[leonorrib]

Thank you for your answer. I'll try what you suggest.

Right, the server is still unavailable. It would be nice to be able to play with threasholds. Could you share the R script?

Best regards

[leonorrib]

Dear @amarinderthind,

Just a kind reminder :) Could you share the R script that you suggested?

Best regards,
Leonor

[amarinderthind]

Hi, @leonorrib I shared the code here https://rpubs.com/amarinder1/deontaminer (Click on the tab to show code; on the right-hand side) and also uploaded the R_decontaminer_visualizationScript
https://github.com/amarinderthind/decontaminer/tree/master/R_decontaminer_visualizationScript

[leonorrib]

Thank you :)