Hi all, I'm trying to use DiffBind in Galaxy to make a PCA or multiple ChIP-seq sets. I have the .bam files and .narrowPeak files for four groups of samples, each with three replicates. I have tried to use the latest version of Diffbind available (Galaxy version 18.104.22.168), as well as a previous version (22.214.171.124).
When using the latest version, I can't figure out how to rearrange my files to input them in the correct order since it states that the input order for the .bam files "MUST match the input order of the peaks files." The input boxes automatically populate and I can't seem to rearrange the list of files into the correct order to match the peak files. Is there a way around this? Also, when I have selected the first two groups of samples and wish to add another two groups, the "Insert Group" button is unclickable and doesn't work, so I can't add more groups/files.
When I execute this analysis using only two groups, I get the beginnings of the PCA I want. So I thought I would try the earlier version to see if that would also work but allow me to add all four groups. It does indeed allow me to add all the groups (and in the correct order), but even when I check yes to "visualizing the analysis results" the only visual output is a heat map, and there's no PCA, which is what I really want.
If anyone has any tips on getting either of these versions of Galaxy to work and give me a PCA for my four sets of samples that would be very much appreciated!! Thank you so much, and sorry if I'm just missing something dumb!