Good time of the day everybody,
Could anybody please advise if I have to discard some of my samples (reads, repeats). Or may be please explain me what could be the reason for the results I see.
I am using Galaxy Libraries: 21 is input; 22, 23, 25 - IPs; 27 is IgG control
I analysed my 150bp paired ChIP-Seq reads: - trimmed (Trimmomatic, details for all used tools are below); - mapped BWA-MEM (hg19 full); - filtered (Filter SAM or BAM) with: - plotFingerprint and; - multiBamSummary->plotCorrelation.
Image results are attached below.
*What could be the reason my IgG control is the same as other two repeats? Why one of my repeats is more different from input or IgG that other repeats? What shall I do with this data?* For example, I can analyse ChIP samples against the input or I can analyse one of my the most different ChIP sample against input or IgG.
Just to note that this ChIP was run in parallel with another ChIP with the same antibody, concentrations etc. There is IgG control is in between of ChIPed DNA and input. But that was mapped against hg38. The image can be found in this post: bamCompare The best normalization for weak signal ChIP-Seq
![plotCorrelation]][1]
Details of the tool settings that were used:
Trimmomatic: SLIDINGWINDOW (number of bases to average across – 4; Average reads score >20); Removed Adapters reference - TrueSeq3 (paired)
BWA-MEM
Using reference genome hg19
Single or Paired-end reads paired
Platform/technology used to produce the reads (PL) ILLUMINA
Filter SAM or BAM
Header in output Include header
Minimum MAPQ quality score 20
Filter on bitwise flag yes
Only output alignments with all of these flag bits set Read is mapped in a proper pair
plotFingerprint default
multiBamSummary default
plotCorrelation Correlation method Spearman
