Hi there! I have a collection of 2 BAM files that I want to pool together in the treatment option for MACS2 callpeaks. I selected the collection as the input for the tool. When I tried this, the output (peaks in tabular format) only had one SRR file name in the peaks ID column. Is this because it didn’t recognize the 2 SRR BAM files in the collection? Or does it just use one BAM name for the peaks? Do I have to select the individual BAM files within the collection (as opposed to the collection) for this to work appropriately? Thanks!
Hello @aperreault
Hopefully you have discovered the option already, but the form can be toggled to inform whether to process each sample individually (not pooled) or to process them together (pooled).
You can use a collection with either.
This is where to find it:
Hope this helps! 