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Modified
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ChIP-seq QC — NSC/RSC (phantompeakqualtools)
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5 items
Peak Calling — MACS3 (CTCF, with control)
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9 items
Motif Enrichment - GimmeMotifs vs JASPAR2020
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7 items
Peak Annotation — ChIPseeker (hg38)
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7 items
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4 items
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May 30, 2026 at 19:49
May 30, 2026
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Regulatory-genomics demo answering the catalogue question 'Which transcription-factor motifs are enriched at these peaks?'.
Dataset: ENCODE CTCF ChIP-seq in GM12878 (lymphoblastoid), experiment ENCSR000DZN, treatment alignments ENCFF033WII with matched input control ENCSR000EYX/ENCFF157YWH — both GRCh38, subset to chromosome 20 to keep the demo small, fast and falsifiable.
Pipeline: MACS3 ChIP peak calling (narrow, with control, -g hs) -> phantompeakqualtools NSC/RSC QC -> ChIPseeker peak annotation (hg38) -> HOMER motif enrichment.
Positive control: CTCF has the single strongest, most reproducible motif in ChIP-seq (~19 bp CCCTC consensus, JASPAR MA0139). The acceptance test is binary — HOMER's known-motif table should list CTCF as the top hit at p < 1e-10.
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