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Tuesday, July 15, 2008

Yet another Chip-Seq tool

One more chip seq tool for the road? How about NPS? It claims to do the the same stuff as findpeaks 1.0, but now with a Laplacian of Gaussian edge detection algorithm bolted on top. (Why? I'm not sure.)

Finding histones isn't exactly rocket science, people. They're pretty easy, and (unlike transcription factors) they saturate very quickly. The trick is to use good alignments, and to get the right fragment length for your reads. If you do that, noise will be limited, and locations are pretty obvious. Paired End Tags completely solves the second problem, and using a good aligner does the first. If you want a good Chip-Seq tool, just write one that uses PET. (Mine's almost done, by the way - just debugging the first test set today.)

Anyhow, it's fun to watch people re-invent the wheel... again and again. Hey, anyone want to write another chip-seq tool? I think we're up to 2 in java and 3 in python, with a few in perl? For something really different, how about brainfuck?


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