Is there any option in annotatePEak (chipseeker) to normalize the reads? · Biostar

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Is there any option in annotatePEak (chipseeker) to normalize the reads?

Hi everyone,

I'm carrying out some ChIP seq analysis. After peak calling with MACS2, I've used annotatepeak (Chipseeker), but regarding the output, I have some questions, that I hope you will answer: -I assume that the column under the name "width" is the read depth for each peak -Are these reads normalized? If the answer is not, how I can normalized them?

Thank you very much in advance

Best

chip-seq chipseeker

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written 9.7 years ago by Lila M

I was under the impression that 'width' actually meant how long the peak was. Also MACS2 comes with a -SPMR flag that can be used to normalize your track files.

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written 9.7 years ago by Sinji

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