New to W-ChIPeaks? Please take a moment to visit our How to Use section.
Due to lack of use, PELT will no longer be supported after November 31. BELT will still be supported.
A Flash-based uploader for BELT is now available for Firefox and Safari users wishing to uploaded files larger than 2GB, as well as for users that experience issues with the CGI-based uploader.
We have noticed several issues with no peaks being called by BELT in BED-formatted files. If you experience this issue, please contact us.
BELT 1.0.1 has been released. The source and Linux x86_64 binaries are available for download, and the other binaries will be compiled within the next few days.
Firefox and Safari appear to improperly handle uploads greater than 2GB, we recommend that a different browser be used with W-ChIPeaks if the data to be uploaded is greater than 2GB.
samtools is used by BELT to convert BAM to SAM, we have added the proper citation here.
Beta support for C. elegans (ce6), D. melanogaster (dm3) and A. thaliana (tair9) has been added to BELT. Please send feedback and report any issues here.
BELT is now available for download as a standalone binary here.
PELT is back online for NimbleGen data only. We hope to restore Agilent array support soon.
The complete list of announcements is available here.
ChIP-based technology is becoming the leading technology to globally profile thousands of transcription factors and elucidate the transcriptional regulation mechanisms in living cells. It has evolved rapidly in recent years, from hybridization with spotted or tiling microarray (ChIP-chip), to pair-end tag sequencing (ChIP-PET), to current massively parallel sequencing (ChIP-seq). Although there are many tools available for identifying binding sites (peaks) for ChIP-chip and ChIP-seq, very few are available as easily-accessible online web tools for processing both ChIP-chip and ChIP-seq for the ChIP-based user community. As such, we have developed a comprehensive web application for processing ChIP-chip and ChIP-seq data. Our web tool W-ChIPeaks employs a probe-based or bin-based enrichment threshold to define peaks and applies statistical methods to control the false discovery rate for identified peaks. The web tool includes two different web interfaces, PELT for ChIP-chip and BELT for ChIP-seq, both of which were tested on previously published experimental data. The novel features of our tool include a comprehensive output for identified peaks in different formats such as GFF, BED, UCSC web browser compatible wiggle (.wig) and bedGraph, annotated genes to which these peaks are related, a graphical interpretation and visualization of the results and a user-friendly web interface.
Please cite the W-ChIPeaks paper if you use this service. Download the paperhere.