ChIP-seq technical replicates giving very different percentage mapping score. Is it normal?

Question

[s.singh]

Hi,

I have two biological replicates of histone ChIP. Each biological replicates has its own technical replicate. I mapped the ChIP reads using bowtie-1 (because I wanted to use -m 2 parameter and it was single end 50 BP long reads). I then removed the PCR duplicates from each of the datasets using "samtools markdup -r" function.

After removing the duplicates, I am seeing a huge difference in the percentage of mapping to the genome between the technical replicates. A table in the link: https://ibb.co/41TzBnn

Is it normal? What could be the cause of such kind of behaviour between the technical replicates?

Thanks, -S

[ATpoint]

What does "technical" mean in this context? What is the organism, these mapping rates are all pretty low.

[s.singh]

Technical replicates in my case are replicates where the biological material is the same but they are sequenced at different times.

The organism is C. elegans. I know the mapping scores are very low. I just feel like it is hard to get a good ChIP all together.