MotifPeeker-reports
Authors: Hiranyamaya (Hiru) Dash, Thomas Roberts, Maria Weinert,
Nathan Skene
Updated: Dec-02-2024
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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Reports
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/)
Built-in data
Dataset Details
Report generated from built-in data, as described in theMotifPeeker vignette.