I have been struggling with running MACS2 for the past two weeks. The software is not producing narrowpeaks results and bed results when adding an input. I am not sure what is the issue and I have tried running it many times with different parameters. I have checked EBI/SRA and the data is loaded correctly, which consists of Input, TEAD1, and TEAD4 immunoprecipitated samples. Could you please provide an insight to the issue? I am obtaining results without an input file, but I know it is not recommended.
The link to my history is below:
https://usegalaxy.org/u/nourmahfel/h/chip-seq
BW,
Nour