ChIP-Seq FAQ (7)

Have a ChIP-seq analysis question? Chances are, we have an answer.

If I have a unique alignment rate of 20%, does that mean my samples are contaminated?

Modified on Thu, 13 Aug, 2020 at 6:06 PM
When spike-in control chromatin cannot be included, what is the best way to normalize two or more samples that have different enrichments and/or different number of reads?

Modified on Thu, 13 Aug, 2020 at 6:19 PM
If my samples don't have a spike-in, is the CHIP-seq data still going to be reliable?

Modified on Fri, 25 Sep, 2020 at 2:59 PM
What is the purpose of motif analysis?

Modified on Fri, 25 Sep, 2020 at 3:09 PM
I want to draw the control and treated samples in the same heatmap. How can I do that?

Modified on Fri, 25 Sep, 2020 at 3:15 PM
Do you recommend any changes in the default settings while doing an analysis for histone modification versus transcription factor?

Modified on Fri, 4 Dec, 2020 at 12:55 AM
Is there a way of looking at both narrow and broad peaks and then merging them?

Modified on Fri, 25 Sep, 2020 at 3:41 PM