Hi, I am new to chips analysis. My aim is to compare the histone marks from two different subtypes of a cancer and want to further integrate these results with the transcriptomic information from the same samples.
I am analyzing my chipseq data enriched for histone marks by using following steps:
- Quality filtering of raw reads,
- Mapping with bowtie,
- Converting to bam, indexing followed by sorting using samtools
- Preprocessing of the aligned reads using deep tools in the following manner
a) Correlation between bam b) Coverage check c) GC bias check and correction
- GC corrected bam was used to generate matrix with reference point using computeMatrix which was followed by plotting the heat map.
In order to do this I have few queries:
A) While using compute matrix from deep tools I am getting so many peaky around the TSS and TES, but normally it should be a sharp peak. Please correct me if I am doing something wrong.
B) How can I integrate MACS2 to call peaks with the above said pipeline.
C) What should be the best practice and how should I proceed to find potential differentially regulated genes or regions.
Any suggestions and help will be highly appreciated.