Hi all of you, I was wondering whether there are any peak finders for transcription factors out there that qualify as good under the following criteria:
* can distinguish between closely adjacent peaks
* identifies peaks with high spatial resolution
* high sensitivity and specificity
* accepts aligned peaks in .bed format
* does not confuse with millions of useless options
* reasonably fast (processes more than 2 million drosophila reads per minute)
* makes full use of input sequencing by subtracting background before peak finding
* free and open source
Have wasted quite some time testing various peak finders and have been very disappointed by everything I looked at. The ones that I have tested include MACS, FindPeaks and PICS.
Wrote my own peak finder today that appears to fulfill all of the above by using a simple strand specific double window scanning approach on background subtracted sample. Appears to work really well and am wondering right now why nobody has done this before.
Would love to hear your opinion on this.
* can distinguish between closely adjacent peaks
* identifies peaks with high spatial resolution
* high sensitivity and specificity
* accepts aligned peaks in .bed format
* does not confuse with millions of useless options
* reasonably fast (processes more than 2 million drosophila reads per minute)
* makes full use of input sequencing by subtracting background before peak finding
* free and open source
Have wasted quite some time testing various peak finders and have been very disappointed by everything I looked at. The ones that I have tested include MACS, FindPeaks and PICS.
Wrote my own peak finder today that appears to fulfill all of the above by using a simple strand specific double window scanning approach on background subtracted sample. Appears to work really well and am wondering right now why nobody has done this before.
Would love to hear your opinion on this.
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