ChIP-Seq Top2 in Yeast
Contents
Introduction
This wiki page combines the two sequencing experiments of ChIP-Seq on yeast samples udring June / July 2017.
Sample quality
In the above previous analyses, we undertook some Duplicate removel as this showed up to be an issue in the FastQC quality files.
However, the effect of this removal was very low. In any case, the MACS2 program takes care of duplicates so samples were only trimmed for adapters and quality.
Alignment to the S288C Reference
Bam quality, no filtering
First Experiment
Second Experiment
Alignment to the new W303 Reference
Bam quality, no filtering
First Experiment
Second Experiment
Bam quality, filtering applied
The bam files were filtered both for mapping quality and low integrity reads in the following manner:
samtools view -b -F 1820 -q 48 <INBAMFILE> -o ${OUTBAMFILE> -@ <NUMTHREADS>
First Experiment
Second Experiment
Bam quality, 2nd filtering applied
This time bam files were filtered to MAPQ 28:
samtools view -b -F 1820 -q 28 <INBAMFILE> -o ${OUTBAMFILE> -@ <NUMTHREADS>
First Experiment
Second Experiment
Differential Peak-calling
Macs2 incorporated differential peak calling somewhat later into its set of tools. The idea is to take two conditions and compare their peaks.
The pipeline to follow is probably Macs2's recommended one at Differntial Binding Events
