Data Output

[benyoung93]

Hi there

First of all thank you for this program, it is providing me with really biological useful results to use in GO and pathway analysis.

One query I have is that clust provides a visualtion (in the form of a pdf) of the coexpressed genes. I want to tidy this up by downloading the data used to plot these graphs in the pdf. Is there a way to do this currently or is there a way to get this data out?

I apologise if this is a basic request or I have missed something already shared, but I appreciate the time foe any response.

Ben Young

[BaselAbujamous]

Hi Ben

Thanks for your question, and I am glad that clust is giving you biologically meaningful clusters.

Inside the output folder there is a folder called "Processed_Data", which includes the gene expression profiles of the data after filtering, replicate summarising, and other pre-processing steps. This data is directly usable to re-plot the clusters using the tool that you like (MATLAB, R, Python, etc). You can find the names of the genes in each cluster in the Clusters_Objects.tsv file. So using these, you can redraw figures as you wish.

Please let me know if you need further assistance in this, and if you do, please let me know which language (e.g. R) you use so I can help you more concisely.

All the best Basel

[benyoung93]

Hi Basel I see. On my initial run I did not get that output. I have re-installed and re-run and now have that output. Re plotting, I am more than able to do this now. From a quick glance I just need to subset the "processed data" using the clusters object file and that is no problem. I am also about to test the functionality of using multiple species which I am super excited about. It will be really interesting to see if the treatment I am interested in has any clusters conserved across multiple coral species. Again, great program and thanks for the time you have put into this !!! Ben