chemistry

Peak calling

Peak calling is a chemistry topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Peak calling rather than just read about it. In short: Peak calling is a computational method used to identify areas in a genome that have been enriched with aligned reads as a consequence of performing a ChIP-sequencing (ChIP-seq) or MeDIP-seq experiment. These areas are those where a protein interacts with DNA.

Key takeaways

Peak calling belongs to chemistry; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Peak calling to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Peak calling from memory before moving on to harder problems.

Reference excerpt

Peak calling is a computational method used to identify areas in a genome that have been enriched with aligned reads as a consequence of performing a ChIP-sequencing (ChIP-seq) or MeDIP-seq experiment. These areas are those where a protein interacts with DNA. When the protein is a transcription factor, the enriched area is its transcription factor binding site (TFBS). Popular software programs include MACS. Wilbanks and colleagues is a survey of the ChIP-seq peak callers, and Bailey et al. is a description of practical guidelines for peak calling in ChIP-seq data.

Methods Peak calling may be conducted on transcriptome/exome as well to RNA epigenome sequencing data from MeRIPseq or m6Aseq for detection of post-transcriptional RNA modification sites with software programs, such as exomePeak. Many of the peak calling tools are optimized for only some kind of assays such as only for transcription-factor ChIP-seq or only for DNase-Seq. However new generation of peak callers such as DFilter are based on generalized optimal theory of detection and has been shown to work for nearly all kinds for tag profile signals from next-gen sequencing data. It is also possible to do more complex analysis using such tools like combining multiple ChIP-seq signal to detect regulatory sites. In the context of ChIP-exo, this process is known as 'peak-pair calling'. A recent benchmarking study compared the performance of several peak calling tools, highlighting the strengths and limitations of each method. This study evaluated peak calling tools including MACS2, SEACR, GoPeaks, and LanceOtron, and provides guidance for selecting appropriate peak callers in CUT&RUN experiments.

Differential peak calling Differential peak calling is about identifying significant differences in two ChIP-seq signals. One can distinguish between one-stage and two-stage differential peak callers. One stage differential peak callers work in two phases: first, call peaks on individual ChIP-seq signals and second, combine individual signals and apply statistical tests to estimate differential peaks. DBChIP, MACS2, and MAnorm are examples for one stage differential peak callers. Two stage differential peak callers segment two ChIP-seq signals and identify differential peaks in one step. They take advantage of signal segmentation approaches such as Hidden Markov Models. Examples for two-stage differential peak callers are ChIPDiff, ODIN. and THOR. Differential peak calling can also be applied in the context of analyzing RNA-binding protein binding sites.

Software This incomplete list includes tools that are commonly used for peak calling in bioinformatics analyses.

p Published as pre-print

See also ChIP-sequencing (ChIP-seq) CLIP-Seq DNA Sequencing

References

External links THOR

Worked examples

Example 1 — a first encounter with Peak calling

Start with the simplest possible case. Write down what Peak calling claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In chemistry, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Peak calling before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Peak calling ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Peak calling

In research: Peak calling appears in chemistry research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Peak calling in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Peak calling is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics, DNA sequencing, Molecular biology techniques, so understanding it makes those chapters shorter.
In everyday life: Look for Peak calling outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Peak calling in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Peak calling means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Peak calling out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Peak calling in simple terms?

Why does Peak calling matter?

Because it connects several chemistry ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Peak calling?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Peak calling.