diffBind analysis: only one replicate
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@danielaperry2015-21742
Last seen 2.1 years ago

Hi there,

I am trying to use diffBind to obtain a set of consensus peaks and fold changes for three different transcription factors chipped. I am comparing WT vs. mut, with one gene knocked out in mutant. For one of the transcription factors, I only have one replicate as the second replicate has failed. As a result, I am getting errors from diffBind. Any advice on how to proceed? Thank you.

diffbind chipseq • 214 views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 15 hours ago
CRUK, Cambridge, UK

Actually, you have no replicates for this TF, only a single sample. Which could be an outlier, you have no way of knowing without replication.

Without replicates you can not do any meaningful statistical analysis. You can do things like look at peak overlaps with other factors, or look at relative enrichment in this sample compared to other peaks identified as being differentially bound. But you can't identify differentially bound peaks for this factor with any confidence.

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