PAVIS is a tool for facilitating ChIP-seq data analysis and hypotheses generation. It offers two main functions: annotation and visualization. The annotation function provides the relative location relationship information between query peaks and genes and other comparison peaks in a genome, and reports relative enrichment levels of peaks in different genomic regions. The visualization offers a simultaneous view of multiple peaks in the context of genomic features and nearby comparison peaks. PAVIS takes as the input the peak location data generated by a peak-calling tool (e.g., MACS). The default format of input peak data files is the UCSC BED format. PAVIS also supports the GFF3 format, and can use peak data files from most ChIP-seq data analysis tools (e.g., EpiCenter).
The last update on 02-05-2018: the genome visualization browser function has been suspended until the related browser issue can be solved. The server has been upgraded with the lastest Python Packages
- Species/Genome Assembly/Gene Set
- specifies the organism/genome assembly version/a particular gene set for the analysis
- Upstream and downstream Length
- Besides gene regions, PAVIS can also annotate peaks in upstream regions of Transcript Start Site (TSS), as well in downstream regions of Transcription Termination Site (TTS). The default upstream length is 5000bp, and downstream length is 1000bp. If you do not want to set a specific limit of a region length, you can sets it to be 0 (No limit), and it will include almost all non-gene regions.
- Peak data file:
- each input peak data file must be a flat or gzipped text file. A gzipped file must have .gz filename extension, and is preferred because it can reduce time to transfer large data over the Internet. The suggested filesize limit for each peak data file is 10 MB.
- File format:
- the default input data file format is the UCSC BED file format. If your file is not in the UCSC BED, the GFF3 or EpiCenter format, you can specify the filed delimiter, and the column numbers of three required fields: chromosome, start position, and end position fields. The column number is the 1-based.
W. Huang, R. Loganantharaj, B. Schroeder, D. Fargo, and L. Li. PAVIS: a tool for Peak Annotation and Visualization. Bioinformatics, 2013, doi:10.1093/bioinformatics/btt520.
contact weichun dot huang at nih dot gov for questions, comments or other feedback.