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  • VeenaV
    replied
    hi Dawe, All,

    I debugged the issue and found that it was basically an issue with the input file fed to MACS.
    I was running MACS on .sam files. The program used to generate signal
    files from .sam files excluded repeats (X:A:R tags), whereas MACS
    included the repeats in the .sam file. I now reran MACS using the bed
    files as input for MACS (instead of .sam files) and it looks fine
    now.

    Thanks,
    Veena

    Leave a comment:


  • dawe
    replied
    Originally posted by VeenaV View Post
    Hi,

    Am using MACS for the first time. I ran MACS on my sequence data and I find peaks (as listed in the bed file) in regions that have no signal. Why would this be? Has anyone encountered this phenomenon before? Please suggest.

    Thanks in advance,
    Veena
    How did you check there's no signal in those regions?

    Leave a comment:


  • VeenaV
    started a topic MACS peaks

    MACS peaks

    Hi,

    Am using MACS for the first time. I ran MACS on my sequence data and I find peaks (as listed in the bed file) in regions that have no signal. Why would this be? Has anyone encountered this phenomenon before? Please suggest.

    Thanks in advance,
    Veena

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