Hi everyone,
I am looking for some advice regarding the analysis of a MeDIP-seq dataset. I generated paired-end sequences of two biological replicates of the same genotype, while just one Input sequence is available.
I was planning to use Seqmonk to have a first glance but despite it's very user-friendly I am having a hard time understanding which tools I should use; in particular, I do not see at which step the Input dataset is taken into account to correct the IP datasets. The only option that makes the distinction between IP and Input seems to be the use of MACS to define probes but I was wondering if the MACS algorithm is good at finding what I expect to be rather wide peaks.
I hope my queston is not too confused.
Thanks in advance.
I am looking for some advice regarding the analysis of a MeDIP-seq dataset. I generated paired-end sequences of two biological replicates of the same genotype, while just one Input sequence is available.
I was planning to use Seqmonk to have a first glance but despite it's very user-friendly I am having a hard time understanding which tools I should use; in particular, I do not see at which step the Input dataset is taken into account to correct the IP datasets. The only option that makes the distinction between IP and Input seems to be the use of MACS to define probes but I was wondering if the MACS algorithm is good at finding what I expect to be rather wide peaks.
I hope my queston is not too confused.
Thanks in advance.
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