Dear all,
I'm using phantompeakqualtools to compute cross-correlation for a set of
different histone modification ChIP-seq data and related input control with
biological replicates.
Since it is the first time I am working on ChIP-seq data, I don't have yet
enough background to be confident in graphes I obtained.
I would like to know :
1) Is it expected to see a peak corresponding to fragment length for the input
data set (i.e. without IP) ?
2) Is the difference between cross-correlation profiles related to biological
replicates sufficient to throw a biological replicate ? Actually, for some of
the histone marks I am analyzing, profile as well as NSC and RNC are really
different between replicates (an example is provided attached), I was wondering
if I should still consider replicates with low NSC/RNC.
Thanks a lot for helping.
Best,
Pierre-François
Original issue reported on code.google.com by pierre-f...@orange.fr on 29 Apr 2015 at 2:16
Original issue reported on code.google.com by
pierre-f...@orange.fr
on 29 Apr 2015 at 2:16Attachments: