ChIP-seq
ChIP-seq (Chromatin ImmunopreciPitation sequencing)
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Objectif |
Mettre en évidence les interactions ADN/protéine à l’échelle du génome |
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Prérequis |
Données issues du séquençage des des fragments isolés par immunoprecipitation de chromatine (ChIP). Pour plus de détails sur le protocole ChIP-seq et pour la liste de publications plus complète, vous pouvez consulter le site d'Illumina. |
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Livrable |
Rapport html : exemple et explications |
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Méthode |
Pipeline nf-co.re/chipseq
Raw read QC(FastQC) / Adapter trimming (Trim Galore!) / Alignment (BWA) / Merge alignments from multiple libraries of the same sample (picard)/ Filtering to remove: reads mapping to mitochondrial DNA (SAMtools), reads mapping to blacklisted regions (SAMtools, BEDTools) ... ,/Alignment-level QC and estimation of library complexity (picard, Preseq) / Create normalised bigWig files scaled to 1 million mapped reads (BEDTools, bedGraphToBigWig) / Generate gene-body meta-profile from bigWig files (deepTools) / Calculate genome-wide IP enrichment relative to control (deepTools) / Calculate strand cross-correlation peak and ChIP-seq quality measures including NSC and RSC (phantompeakqualtools) / Call broad/narrow peaks (MACS2) / Annotate peaks relative to gene features (HOMER) / Create consensus peakset across all samples and create tabular file to aid in the filtering of the data (BEDTools) / Count reads in consensus peaks (featureCounts) / Differential binding analysis, PCA and clustering (R, DESeq2) |