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2. Mapping
Mapping to genome reference performed using BWA.
- Deliverables:
- Mapping results, as bam files and mapping statistics.
- Tools Used:
- BWA: (Li 2013) primary aligner used to generate read alignments.
- Samtools: (Li 2009) used to prepare bams and generate mapping statistics.
4. Peak Calling
Counting the number of normalized ChIP-seq reads compared to a background control (Input or mock ChIP) to identify regions of binding enrichment.
- Deliverables:
- Peak calls as narrowPeak (BED 6+) files, containing p-value, q-value, and fold enrichment scores for each peak.
- Per-base normalized signal files as bigWigs.
- Tools Used:
- MACS2: (Zhang, 2008) used to identify and score peak regions.
- bedtools (Quinlan, 2010) used for optional blacklist filtering.
5. Significance Threshold Analysis
Statistical analysis and informed heuristics to determine appropriate significance threshhold(s) for identifying peaks for downstream analysis.
- Deliverables:
- Summary file outlining peak counts at selected levels (High, Medium, and Low stringency) and master file containing counts over a wide range of q-values and fold enrichment values. Peak count vs q-value and fold enrichment plots.
- Tools Used:
- R, and in-house scripts and ggplot: used to produce peak count statistics and plots.
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