gappedPeak

[xi wang]

Currently, we are looking at different histone markers with ChIP-seq, and found the method posted by Dr. Anshul Kundaje very useful: https://sites.google.com/site/anshulkundaje/projects/encodehistonemods However I just had a question about gappedPeaks. 

According to the post, gappedPeaks were defined as broadPeaks that contain at least one strong narrowPeak. However, I found the gappedPeaks output by MACS2 didn’t follow this definition, as the gappedPeaks were exactly the same as broadPeaks. I am just wondering if I did something wrong with MACS2 or postprocessing needs to be carried out on MACS2 results. 

Many thanks! 

[Jin]

Hello Xi Wang,

Yes, this is MACS2 issue. We already knew about this so our latest version of the pipeline does not generate gappedPeak and broadPeak.

Thanks,

Jin

--
You received this message because you are subscribed to the Google Groups "idr-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to idr-discuss+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.