Tweet
Hi there,
I am having trouble to visualize my Chip-Seq peaks called by MACS in two subsequent biological replicates.
I let MACS generate wiggle files of the peaks that I could use individually for visualization, but ideally I would like to look at only the peaks that have been found in both replicates and throw out anything that is only found in one of them.
So, I took the bed files generated by MACS, concateneated them and clustered any regions overlapping by 1 bp from both replicates into 1 region which should give me only the peaks found in both replicates.
However, when I load the bed files into my prefered genome browser (zenbu), for each peak I can only get (as opposed to the wig files) a bar that covers the region, but no quantity of tags or signal or whatever.
So how do people show those beautiful peaks in all the papers that have those nice peak shapes? What kind of file should be used for that?
Thank you very much for your help!
Cheers,
Tobias
I am having trouble to visualize my Chip-Seq peaks called by MACS in two subsequent biological replicates.
I let MACS generate wiggle files of the peaks that I could use individually for visualization, but ideally I would like to look at only the peaks that have been found in both replicates and throw out anything that is only found in one of them.
So, I took the bed files generated by MACS, concateneated them and clustered any regions overlapping by 1 bp from both replicates into 1 region which should give me only the peaks found in both replicates.
However, when I load the bed files into my prefered genome browser (zenbu), for each peak I can only get (as opposed to the wig files) a bar that covers the region, but no quantity of tags or signal or whatever.
So how do people show those beautiful peaks in all the papers that have those nice peak shapes? What kind of file should be used for that?
Thank you very much for your help!
Cheers,
Tobias