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update README
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sreichl committed Sep 14, 2024
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Expand Up @@ -91,14 +91,10 @@ The processing and quantification described here was performed using a publicly

> [!IMPORTANT]
> **Duplciate reads** can be filtered during the alignment step by `samtools` and/or ignored during peak calling by `MACS2`.
>
> The inclusion of duplicates should be intentional, and may lead to a large number of consensus regions.
>
> The removal of duplicates should be intentional, might remove real biological signal.
>
> The decision depends on your downstream analysis steps e.g., rigorous filtering (e.g., using `edgeR::filterByExpr`) and/or accounting for PCR bias by normalization conditional on genomic region length and GC content (e.g., [CQN](https://academic.oup.com/biostatistics/article/13/2/204/1746212)) and goals (e.g., differential accessibility analysis).
>
> We recommend reading this ChIP-seq tutorial's section on ["Removing redundancy"](https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html).
> **The inclusion of duplicates** should be intentional, and may lead to a large number of consensus regions.
> **The removal of duplicates** should be intentional, might remove real biological signal.
> **The decision depends** on your downstream analysis steps e.g., rigorous filtering (e.g., using `edgeR::filterByExpr`) and/or accounting for PCR bias by normalization conditional on genomic region length and GC content (e.g., [CQN](https://academic.oup.com/biostatistics/article/13/2/204/1746212)) and goals (e.g., differential accessibility analysis).
> **We recommend** reading this ChIP-seq tutorial's section on ["Removing redundancy"](https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html).
# 🛠️ Usage
These steps are the recommended usage for this workflow:
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