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If I have a unique alignment rate of 20%, does that mean my samples are contaminated?
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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?
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If my samples don't have a spike-in, is the CHIP-seq data still going to be reliable?
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What is the purpose of motif analysis?
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I want to draw the control and treated samples in the same heatmap. How can I do that?
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Do you recommend any changes in the default settings while doing an analysis for histone modification versus transcription factor?
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Is there a way of looking at both narrow and broad peaks and then merging them?