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

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?

chip-seq mapping
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updated by Mikael Huss Mikael Huss • written by Jordan Jordan

2 answers

  • 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!

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written by k.nirmalraman k.nirmalraman

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.

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written by Jordan Jordan

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.

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written by Mikael Huss Mikael Huss

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.

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written by Jordan Jordan

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