Which peak-finder after bowtie? Chip-seq

[sbrohee]

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.

[ETHANol]

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

[mudshark]

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

[Alexei]

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.

[sbrohee]

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