With all the ChIP peak-calling tools floating around, especially ChIP-seq, we thought maybe we should throw our hat in the ring here as well 
BTW, the information on this site's been helpful several times!
W-ChIPeaks (PMID: 21138948) is a Web-based application for ChIP-chip and ChIP-seq peak calling. The ChIP-chip tool, PELT (Probe-based Enrichment Level Threshold), will call peaks in .GFF formatted NimbleGen tiling and NimbleGen/Agilent promoter array output at the 95%, 98% and 99% confidence level. The ChIP-seq tool, BELT (Bin-based Enrichment Level Threshold), provides powerful peak calling capability with a variety of customizable parameters, including calling peaks at a desired FDR. PELT accepts 500MB, divided among a maximum of eight .GFF files. BELT accepts 3GB, divided between the treatment and optional control file, although it allows .zip and .tar.gz compressed archives (each with a maximum 4GB uncompressed file size). We provide easy-to-use Web interfaces for both PELT and BELT, and Web display of results with a graphical survey of called peaks (output in .WIG or .bedGraph is available for use in IGB or UCSC). In addition, we will soon release the standalone peak-calling portion of BELT once it is authorized by our university’s licensing department (it and its C++ source code will be free to download, use, modify and share).
We understand that W-ChIPeaks got off to a somewhat rough start when we first released the tool, as anyone here who tested it may have found. However, we have found and fixed many bugs, improved the documentation and migrated to a more powerful server with a larger hard drive, and we believe that W-ChIPeaks is currently a more polished and reliable product than its first release.
We hope that PELT and BELT may be useful tools for the ChIP-chip and ChIP-seq community. If anyone tests or uses W-ChIPeaks, please send us your feedback, to improve W-ChIPeaks and any future web applications that our lab may release, and to stamp out any bugs that remain. I (a second-year undergrad) would also appreciate your feedback with W-ChIPeaks to improve my skills in bioinformatics, programming and Web design.
Thank you for your time and consideration.
Sincerely, Russell Bonneville
BTW, the information on this site's been helpful several times!W-ChIPeaks (PMID: 21138948) is a Web-based application for ChIP-chip and ChIP-seq peak calling. The ChIP-chip tool, PELT (Probe-based Enrichment Level Threshold), will call peaks in .GFF formatted NimbleGen tiling and NimbleGen/Agilent promoter array output at the 95%, 98% and 99% confidence level. The ChIP-seq tool, BELT (Bin-based Enrichment Level Threshold), provides powerful peak calling capability with a variety of customizable parameters, including calling peaks at a desired FDR. PELT accepts 500MB, divided among a maximum of eight .GFF files. BELT accepts 3GB, divided between the treatment and optional control file, although it allows .zip and .tar.gz compressed archives (each with a maximum 4GB uncompressed file size). We provide easy-to-use Web interfaces for both PELT and BELT, and Web display of results with a graphical survey of called peaks (output in .WIG or .bedGraph is available for use in IGB or UCSC). In addition, we will soon release the standalone peak-calling portion of BELT once it is authorized by our university’s licensing department (it and its C++ source code will be free to download, use, modify and share).
We understand that W-ChIPeaks got off to a somewhat rough start when we first released the tool, as anyone here who tested it may have found. However, we have found and fixed many bugs, improved the documentation and migrated to a more powerful server with a larger hard drive, and we believe that W-ChIPeaks is currently a more polished and reliable product than its first release.
We hope that PELT and BELT may be useful tools for the ChIP-chip and ChIP-seq community. If anyone tests or uses W-ChIPeaks, please send us your feedback, to improve W-ChIPeaks and any future web applications that our lab may release, and to stamp out any bugs that remain. I (a second-year undergrad) would also appreciate your feedback with W-ChIPeaks to improve my skills in bioinformatics, programming and Web design.
Thank you for your time and consideration.
Sincerely, Russell Bonneville