Is It Normal To Have Very Low Mapping For Treatment File When Compared To Control File In Chip-Seq?

Question

[Jordan]

Hi,

I'm working on chip-seq and it looks like I have an issue. I'm not sure if it's normal for a chip-seq analysis.

I have a control and treatment file (in fastq format), which I mapped it using Bowtie2. The problem here is, while the input file has 90% mapped, treatment has only 10% mapped (mapping statistics by samtools flagstat option). Is it something I should be worried about?

Answer 1

[k.nirmalraman]

• Did you also perform read quality analysis? you may wanna try FASTQC.
• You may also think about your library preparation protocols?

Do you expect such a drastic difference from your treatment... I hope not, so this is definitely worth investigating!

[Jordan]

I already did the FASTQC analysis before mapping. The reports looked fine. Hence, the bemusement! Since, this was my first time doing chip-seq, I'm not sure what kind of bam files to expect. So, I wanted to know if normally treatment files lower mapping percentage than control files.

Answer 2

[Mikael Huss]

It could be adapter contamination that is giving you a poor mapping rate. Try to look for adapters with FastQC (the program that k.nirmalraman already suggested) and trim them if they are present in a lot of reads.

[Jordan]

I don't think there is an adapter contamination in the fastq file. I already did the FastQC analysis and double checked it now as well too.