fastqc of chipseq dataset - two peaks in GC content
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3.2 years ago
Assa Yeroslaviz ★ 1.7k

We are running a ChIP-Seq experiment of multiple samples on one flow cell. when looking at the fastqc results of the samples, they all look strange.

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both overrepresented adapter and adapter content are in the green and sow no accumulation.

Can anyone explain this kind of behavior? Are these contaminations?

thanks

fastqc GC content ChIP-Seq peaks • 1.6k views
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Have you scanned/trimmed this data? Is it from a 2-color chemistry sequencer (e.g. NovaSeq/NextSeq).

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I haven't trimmed it yet. the sequencing was done a a nextseq with dual indexing.

About the trimming - do I just trim the first bases of the read (hard trim) or should I look for the barcodes (soft trim)?

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Looks like you have a significant number of reads that may just be poly-G (certainly start with G, no signal = G) and those should be removed. Before you do any directed trimming why not just look for adapter sequence and see what happens. Any scan/trim program should work. Post plots after trimming.

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This I have also considered, but why don't I see it also in the overrepresented sequences section? Is it possible that the adapter are so GC (or more G)-rich, that it skew the results so much?

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Can we see what we get post-trimming? FastQC samples data for some of the features it looks at and does not include the entire dataset.

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