First time I have run MACS using Galaxy. I tried to DL the MACS paper from the web site but the link is dead.
I have two experimental ChiPseq data sets and 1 input control for these two datasets. After running bowtie, I used MACS for peak calling. File numbers for the experimental data are 35 and 37, the input control was file number 36.
Can someone please explain the wig files generated by MACS as for as the file nomenclature:
First output I got was: MACS on data 36 and data 37 (control:wig)
Next output I got was MACS on data 36 and data 37 (treatment:wig)
Is the wig file for the first output the input peaks? likewise is the second output (treatment:wig) the peaks for the experimental data set associated with file 37?
Final question is why MACS generated two separate control:wig outputs for data sets 35 and 37 as the same input was used for both data sets.
Thanks in advance for the explanations Scott