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  • Threshold to filter MACS peaks

    Hi everyone,

    I have performed a peak call with MACS on an atac-seq dataset. The results show a large number of peaks, and I was thinking on eliminating some based on the p-value, q-value or other parameter, before proceeding with the motif analysis.

    The problem is, I have no previous experience with NGS data, and so I don't know which is the best parameter to filter and what would be an appropiate threshold. I have tried to find papers regarding this question but I haven't been able to.

    Anyone with experience in the matter could give some advice?

    Thanks in advance

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