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
2. ChIPSeq2
   ENCODE Accession: ENCFF411OOS
3. ChIPSeq3
   ENCODE Accession: ENCFF091ODJ
4. TIPSeq
   Alignment file produced by running the nf-core/cutandrun pipeline on the raw sequencing data sourced from NIH Sequence Read Archives ID: SRR16963166.

Peak calling was performed using MACS3 using the following commands:

## 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
2. CTCFL motif MA1102.3

 Code

Built-in data

Dataset Details

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

 Code