ChIP-Seq FAQ
Have a ChIP-seq analysis question? Chances are, we have an answer.
That could be one of the causes, but it could be other issues as well. An example Sankey Plot of a poor quality sample with 80% unaligned reads. 1. Inc...
Thu, 13 Aug, 2020 at 6:06 PM
As a reminder, a spike-in is a fixed amount of DNA that’s added to all your samples. This allows for a more quantitative comparison across samples and allow...
Thu, 13 Aug, 2020 at 6:19 PM
One of the main purposes of a spike-in is so you can compare global changes in CHIP-seq signal. However, a large amount of researchers who work with ChIP-se...
Fri, 25 Sep, 2020 at 2:59 PM
The input to the motif analysis is a set of peaks. When you're doing the motif analysis, you're trying to find if there's particular motif enric...
Fri, 25 Sep, 2020 at 3:09 PM
Basepair generates a heatmap automatically for you that includes both the treated and control samples. In the heatmap above, the IP and input s...
Fri, 25 Sep, 2020 at 3:15 PM
The type of protein and modification you look at can result in different types of peaks, like narrow versus broad peaks. Transcription factors tend to be na...
Fri, 4 Dec, 2020 at 12:55 AM
At the moment, MACS2, the tool we use for peak calling, does not offer this feature and can only look at just broad or narrow peaks. But the great thing abo...
Fri, 25 Sep, 2020 at 3:41 PM