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  • Which peak-finder after bowtie? Chip-seq

    Hi all,

    Which peak-finder tool would you advice me use after having mapped the sequences on the genome with bowtie --best?

    Thank you all.

  • #2
    It depends on your data. MACS seems to be the most popular, so it's not a bad place to start.
    --------------
    Ethan

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    • #3
      the peak finders least sensitive to sequencing depth in my hands are SISSR and QuEST.

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      • #4
        Macs is a solid place to start..robust, verbose and well-document.

        On the question of the best one, that really depends on your needs/metrics.

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        • #5
          Thanks a lot for the hints! I will look at them!

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