What is PIPA?
PIPA is primarily a tool for the analysis of RNA-seq transcriptomics data. The pipeline connects and integrates freely available next-gen sequencing (NGS) bioinformatics tools with data management capabilities in the form of an accessible and easy to use client (Flash) / server (Python) platform.
Figure 1: Data annotation and management (left) and visualization of read alignments in JBrowse (right)
Because initial development was focused on the analysis of RNA-seq data, the current pipeline offers basic bioinformatics workflows like:
- Upload of experimental data in FASTA/FASTQ format (Illumina) and annotation
- Alignment of reads to a reference genome using Bowtie
- Search of differentially expressed genes using baySeq
- ChIP-seq peak finding with MACS
- Visualization of alignments and other results with JBrowse (which we also help improve)
- Easy accessibility of data/results over simple APIs
- Homo sapiens, available at UCSC: hg19
- Mus musculus, available at UCSC: mm9
- Dictyostelium discoideum, available at: dd on dictyBase
- Dictyostelium purpureum, available at: dp on dictyBase
We structured the pipeline with flexibility in mind so adding new reference genomes and analysis is in reach for current and future developers.
Explorative web interfaces
PIPA is unique in the way it handles time-series (or other sequential) data. In 2009 we started a new paradigm of web gene expression profile analytics with dictyExpress. PIPA upgrades the features of profile analytics by giving users capabilities to define their own gene expression profiles from RNA-seq data and later explore the results in a rich web interface called dicty5.