I am a bit stuck on how to analyze MBD-Seq data starting from fastq.gz files.
I have got MBD-Seq data for a bunch of samples in different conditions and my goal is to reveal differences between them.
Is there anyone who could point me in the right direction to do this? I have done some checking on softwares like MEDIPS or ramwas, but I am not even sure they are 100% appropiate for my case and I get stuck at some point when trying to use them on my data.
Hope anyone can help...thank you!