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Old 10-03-2011, 08:04 AM   #1
sbrohee
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Default 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.
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Old 10-03-2011, 08:41 AM   #2
ETHANol
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It depends on your data. MACS seems to be the most popular, so it's not a bad place to start.
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Old 10-04-2011, 12:41 AM   #3
mudshark
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the peak finders least sensitive to sequencing depth in my hands are SISSR and QuEST.
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Old 10-04-2011, 07:11 AM   #4
Alexei
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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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Old 10-12-2011, 06:29 AM   #5
sbrohee
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Thanks a lot for the hints! I will look at them!
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