ChIP-seq for H3K4me3 and H3K27ac for craniofacial tissue collection from day of birth dunnart (_Sminthopsis crassicaudata_) pouch young.
# Experimental Design
## Experimental Design
__H3K4me3__
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@@ -102,7 +102,7 @@ sample ID | replicate pool | pull down | concentration (ng/uL)| amount (
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# Data Analysis
## Data Analysis
Library construction and sequencing performed by GENEWIZ.
Raw data (Pass Filter Data) was processed by adapter trimming and low quality read removal using NGS quality control software Cutadapt (v1.9.1) to generate clean data for subsequent analysis. software:Cutadapt(version 1.9.1) The process includes the following steps:/
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@@ -148,3 +148,16 @@ Column explain:\
(5) Q20, Q30: The percentage of bases with quality scores (Qphred) higher than 20 or 30\
(6) GC%: The percentage of G+C in the reads\
(7) N(ppm): The number of base ‘N’ per million bases.\
### 1. FastQC on raw reads
### 2. Alignment
### 3. Filtering
### 4. Alignment QC & Library Complexity
### 5. deepTools
### 7. phantomPeakQuals
### 8. Call narrow peaks (MACS2)
### 9. Create consensus peaksets
### 10. Annotate peaks relative to gene features (HOMER)
### 11. Present QC for raw read, alignment, peak-calling in MultiQC
