Has anyone used the Software MM-Chip? http://www.biomedcentral.com/content/pdf/gb-2011-12-2-r11.pdf
I am interested in performing a Meta-analysis of several Chip-Seq results using GEO SRA data (same cell-type, platform and conditions, but different labs) to look for enriched peaks for a few TFBSs. I am considering MM-Chip for this, however, I have a basic question about how to handle study replicates.
Is it standard to input each study replicate as an individual experiment, or pool the reads from the replicates and enter them as one experiment. I have been unable to find any tutorial or info on MM-Chip, so thought I'd see if anyone has any experience with it. Given that MM-Chip will integrate all datasets, I'm uncertain of the protocol.
I have used FASTQC to QC the datasets and bowtie to align them to the genome. If pooling replicates is the way to go at which step should pooling occur?