ChIP-seq normalization, Signal-to-Noise different between samples
I have ChIP-seq data for several time points after a stimulus, but it seems like my samples have differences in signal-to-noise ratio. i.e. some samples have a more background reads relative to reads in peaks than others, likely due to technical variation. Is there a standard way to normalize for this?
Maybe something like MAnorm? But does that work when comparing more than two samples?
• 2,686 views
•
link
written
by
Kelsey Tyssowski •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
written by jared.andrews07
-
Normalization of ChIP-seq results with deepTools
written by Daria •
-
RiP RLE normalisation using spike-in peaks in DiffBind for ChIP-seq
written by spg •
-
Normalize ChIP-seq samples with different signal-to-noise ratio
written by maria.soler •
-
Normalize BigWig's for # of reads in peaks and sequencing depth
written by Zeel •
-
Input control for ChIP-seq. [Seeking for the clarification between "Library DNA conc.", "no. of raw…
written by chiefcat
-
How quantitative is Chip-seq?
written by YanO
-
batch effect for ChIP-seq data
written by Ming Tommy Tang
-
Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal With The Merged Peaks …
written by Nick
-
Manorm For Differential Histone Binding In Chip-Seq Samples
written by Diana
Have a look at the SES normalization method in bamCompare from deepTools. It will take SNR into account when normalizing to input.