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Wednesday, July 23, 2008

100 blog post - Findpeaks 4

Wow.. quite the milestone! 100 blog posts. I never thought I could ramble on this long... well, on second thought, I guess it's not THAT much of a surprise if you know me. (=

Anyhow, I suppose I have a second milestone to talk about as well. I just preformed the first successful FindPeaks 4.0 (pre-alpha??) run using a Paired End MAQ .map file. Why is that important? First, I'm using a binary .map file, which means we don't need to store .mapview files - though, this is a bit of trickery. I now store .bed files instead, which have the added advantage of being viewable through the UCSC browser, while mapview files can't. Second, it's a Paired End ChIP-Seq run. We've been waiting a long time to have paired end chip-seq, so that we'll know where the second end of the tag is. We can now start pinpointing the location of the protein-dna interaction with much greater confidence.

The important thing is that I can now start doing-away with the crazy distributions that single end tags forced upon us. No more X-sets, adaptive distributions or triangle distributions! Yay! (It might still be publishable, but I think the window for that is closing.... another story for another day.)


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