Define exact peak borders

Question

[ATpoint]

Hello,

I would like to ask if there is an implementation to define peak borders. To make it more clear, see this screenshot. I have some reference region from another assay (blue bar on top). Within this region, I check the signal of a second assay (blue peak profile). The question is now if there is a simple solution to define the peak borders (red bar) automatically. MACS does this nicely with the --nomodel option, but as it checkes the input data for significances etc. it does not output all the regions I am interested in. Is there a standalone solution for this task?

[BioinfGuru]

To clarify: you want the red bar to be the same length as the blue bar or as the blue peak region?

What about peak center +/- total fragment length?

More importantly....what is the purpose of defining the borders? what are you trying to achieve by doing this?

[ATpoint]

The read bar is what I printed in by hand, but I would like to get it automatically, based on the shown peak profile. I have a list of mutations. Many of them are within the blue-bar region, but outside of the actual peak signal (so the read bar). In order to exclude these, I would like to have exact borders, in order to exclude these passengers.

Answer 1

[Charles Plessy]

There are many alternative peak callers, but among them perhaps you can have a look at paraclu.

Since it outputs nested clusters, you can define by yourself a threshold that corresponds to granularity that suits the most your analyses. Also, you can run it in a way that all the data will be part of at least one cluster (unlike in the example above, where a small peak is left out).

[ATpoint]

I will check it out, thank you. Cluster within cluster seems to be pretty much what I need.