MotifPeeker-reports

Authors: Hiranyamaya (Hiru) Dash, Thomas Roberts, Nathan Skene
Updated: Jul-16-2024

MotifPeeker-reports is a public archive for interactive HTML reports generated by MotifPeeker, along with the code used to produce them.

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CTCF ChIP-seq - TIP-seq

Dataset Details Compares three public ChIP-seq datasets against a TIP-seq dataset for CTCF in HCT116 cells. Details of the datasets used are as follows: 1. ChIPSeq1 ENCODE Accession: [ENCFF172XLC](https://www.encodeproject.org/files/ENCFF172XLC/) 2. ChIPSeq2 ENCODE Accession: [ENCFF411OOS](https://www.encodeproject.org/files/ENCFF411OOS/) 3. ChIPSeq3 ENCODE Accession: [ENCFF091ODJ](https://www.encodeproject.org/files/ENCFF091ODJ/) 4. TIPSeq Alignment file produced by running the [`nf-core/cutandrun`](https://nf-co.re/cutandrun/) pipeline on the raw sequencing data sourced from *NIH Sequence Read Archives* [*ID: SRR16963166*](https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR16963166&display=metadata). Peak calling was performed using [`MACS3`](https://github.com/macs3-project/MACS) using the following commands: ``` r ## For ChIP-Seq datasets MACSr::callpeak( tfile = ..., cfile = NULL, # No control file nomodel = FALSE, qvalue = 0.01, format = "BAM", name = "chipseq", outdir = ... ) ## For TIP-Seq dataset MACSr::callpeak( tfile = tipseq_alignment_data, nomodel = TRUE, qvalue = 0.01, shift = -75, # 5' shift extsize = 150, keepduplicates = "all", format = "BAM", name = "tipseq", outdir = ... ) ``` Motif files used: 1. CTCF motif [MA1930.2](https://jaspar.elixir.no/matrix/MA1930.2/) 2. CTCFL motif [MA1102.3](https://jaspar.elixir.no/matrix/MA1102.3/)

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Built-in data

Dataset Details Report generated from built-in data, as described in the MotifPeeker vignette.

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