Genetrack-Indexer/Peakpredictor

Question: Genetrack-Indexer/Peakpredictor

7.1 years ago by

Hi everybody, I'm using the Genetrack-Peak-Predictor to predict nucleosome positions. I still have some questions: 1) Am I correct that the genetrack indexer seems to be down on the Public Galaxy Server? I get a server error, when I start it. (The Genetrack Browser doesn't work either; although I'm still not quite sure whether there are dependencies.) 2) By now, I know one paper on Genetrack - http://bioinformatics.oxfordjournals.org/content/24/10/1305.short and I found the following presentation slides: http://ged.msu.edu/angus/tutorials-2011/files/lecture-chipseq.pdf. Galaxy tells me to "cite Blankenberg D, et al. In preparation." Is there additional information? It would be great to know how exactly the peak predictor works, but the slides give only a kind of overview, but of course no explaining and no details and the paper isn't that clear. Thanks, Steffi/ ///

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modified 7.1 years ago by Daniel Blankenberg ♦♦ 1.7k • written 7.1 years ago by Stefanie Ververs • 10

7.1 years ago by

Daniel Blankenberg ♦♦ 1.7k

United States

Daniel Blankenberg ♦♦ 1.7k wrote:

Hi Steffi, GeneTrack should be working again on the Main server, thanks for reporting the error. For information on the inner workings of GeneTrack, you should consult the paper that you mentioned, along with http://genetrack.bx.psu.edu/ and you can additionally contact the GeneTrack author, who I've CC'd here. Thanks for using Galaxy, Dan

ADD COMMENT • link written 7.1 years ago by Daniel Blankenberg ♦♦ 1.7k

Hello Everyone, I think in general you should make sure to cite the authors of the original publication in addition to Galaxy, the note in Galaxy should make this explicit. Small tidbits that may be useful. There is a command line version for genetrack with its source code at: https://github.com/ialbert/chipexo this is a fork of my son's project while he rotated in a lab, he ported a number of tools including GeneTrack to a command line interface. Seems to work well but I have not ran it for large genomes. In the course that I teach the lectures covering ChipSeq analysis: 19, 20 and 21 cover the usage and principles of GeneTrack (among other topics) http://bcc.bx.psu.edu/courses/597D-2011/index-597D-2011.html best regards, Istvan -- Istvan Albert Associate Professor, Bioinformatics Pennsylvania State University http://www.personal.psu.edu/iua1/

ADD REPLY • link written 7.1 years ago by Istvan Albert ♦ 250

7.1 years ago by

Daniel Blankenberg ♦♦ 1.7k

United States

Daniel Blankenberg ♦♦ 1.7k wrote:

Absolutely agree, the citations are arguably the most important part. The GeneTrack paper citation is currently listed in the help for the tools at http://usegalaxy.org and in -central. Any place where a citation is missing is an error and will be corrected as soon as it is reported. Thanks for using Galaxy, Dan

ADD COMMENT • link written 7.1 years ago by Daniel Blankenberg ♦♦ 1.7k

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