I am analysing ChIPseq data on Galaxy beginning with raw fastq files (fastqc, trimmer by column, bowtie2, RmDup, Filter, bamcoverage, merge bam files + bamcoverage of merged files, MACS2 peak calling) and ending up with nice bigwig and bed files for visualizing in IGV. In the end, the goal would be to obtain a list of differentially bound regions because I am comparing wt with ko tissue. I found the nice sounding tool " DiffBind differential binding analysis of ChIP-Seq peak data " on Galaxy and I did this once with RStudio a couple of years ago, but unfortunately I have really problems picking the right bam files for that. Are those the one after "Filter"? The tool at Galaxy leaves me always with "tool error" and "This job was terminated because it used more memory than it was allocated. Please click the bug icon to report this problem if you need help."
Could somebody please help me with that?
Thank you very much in advance!!!
Best wishes, Franziska