A efficient peak finder for high coverage ChIP-seq experiments, written in python.
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The pique package is a high efficiency peak finder for ChIP-seq experiments that yield high coverage allignments to the reference genome. It was developed for studying gene expression in Halobacterium salinarum sp. NRC1, sequenced using barcoded 40bp Illumina reads as part of an ongoing project in Marc Facciotti's lab at UC Davis. INSTALLING ---------- Do the usual python thing. $ cd pique $ python setup.py install --prefix=/someplace/PYTHONPATH/knows/about TESTS ----- Tests are designed to be used with nose. http://somethingaboutorange.com/mrl/projects/nose/ The tests (stupidly) depend on hard-coded paths to find the test data files, so you have to run nosetests from the main module directory (i.e., the one that has setup.py in it). $ cd pique $ nosetests USAGE ----- The workflow pique is designed for goes something like this :  Perform a chromatin immunoprecipitation, extract the DNA, put it in the sequencing machine, get sequence data back.  Align the reads to the reference genome of your organism.  Generate coverage tracks for the forward and reverse strands for the ChIP data and for the controls. You did remember to do controls, right?  Some regions of the genome may be repetitive or ambiguous, such as IS elements. Create a masking file for these regions.  Use a genome browser to select some regions that are definitely not peaks. Make a bookmark file.  Run piquify.py to generate normalized background tracks using the bookmarked non-peak regions.  Run piquant.py to find the noise threshold.  Run pique.py to build a bookmark file of putative enrichment regions.  View the bookmarks in your favorite genome browser (pique was designed around the Gaggle Genome Browser). Delete false positives, manually add false negatives, and adjust any start:stop coordinates that look badly off. Save the bookmark file.  Run piquancy.py to re-annotate the curated bookmark file with enrichment ratios.  Run piquilate.py to re-annotate the curated bookmark file with genes likely to be associated with the enrichment site. CAVEATS ------- Binding coodinates : The peak calling step (pique.py) will attempt to calculate a binding coordinate for the putative peaks it finds. The method used is extremely naive, but we find that it generally comes within about 40bp of the expected binding site. Double peaks : Some enriched regions contain two binding sites, but the algorithm is unable to de-convolute them. We have tried running these regions through several other peak callers with little success. We have included a script for identifying sites that are likely to be double peaks to assist with curation. CONFIG FILES ------------ INSPIRATIONAL QUOTE ------------------- I met men at every turn who owned from one thousand to thirty thousand "feet" in undeveloped silver mines, every single foot of which they believed would shortly be worth from fifty to a thousand dollars—and as often as any other way they were men who had not twenty-five dollars in the world. Every man you met had his new mine to boast of, and his "specimens" ready; and if the opportunity offered, he would infallibly back you into a corner and offer as a favor to you, not to him, to part with just a few feet in the "Golden Age," or the "Sarah Jane," or some other unknown stack of croppings, for money enough to get a "square meal" with, as the phrase went. And you were never to reveal that he had made you the offer at such a ruinous price, for it was only out of friendship for you that he was willing to make the sacrifice. Then he would fish a piece of rock out of his pocket, and after looking mysteriously around as if he feared he might be waylaid and robbed if caught with such wealth in his possession, he would dab the rock against his tongue, clap an eyeglass to it, and exclaim: "Look at that! Right there in that red dirt! See it? See the specks of gold? And the streak of silver? That's from the Uncle Abe. There's a hundred thousand tons like that in sight! Right in sight, mind you! And when we get down on it and the ledge comes in solid, it will be the richest thing in the world! Look at the assay! I don't want you to believe me—look at the assay!" Then he would get out a greasy sheet of paper which showed that the portion of rock assayed had given evidence of containing silver and gold in the proportion of so many hundreds or thousands of dollars to the ton. I little knew, then, that the custom was to hunt out the richest piece of rock and get it assayed! Very often, that piece, the size of a filbert, was the only fragment in a ton that had a particle of metal in it—and yet the assay made it pretend to represent the average value of the ton of rubbish it came from! - Mark Twain, Roughing It LEGAL STUFF ----------- Copyright (c) 2011, Russell Neches All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the University of California, Davis nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. 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