ChIPseeker missing first peak in the interval file?

I used MACS2 to call peak and obtained a narrow peak bed file with 30169 regions but after I input the sequence into chipseeker it shows it still have 30169 regions but when I view the interval file of annotation it has a header but the first peak is lost, when i sort the peaks the first one is peak_2 but peak 1 was in the result of the macs2

Hi @Emilyet

Maybe there was some input problem?

The ChipSeeker tool form has an option near the top that informs the tool about whether the input has a header or not. Make sure that matches your data.

The other thing I can think of is this: MACS2 will happily output data that extends beyond the ends of chromosomes. Other tools will complain or ignore regions that extend past the ends.

Check those two items first, and we can follow up as needed. We’ll need an example shared back for a closer review. Search this forum with “sharing your history” if you are not sure how to do that.

Hi Jenn
Thanks I’ve solved it by using the tabular output of MACS2 instead of narrowpeak file

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