Fish the ChIPs (FC) is an automated computational pipeline aimed at a broad public of users and designed to perform complete ChIP-Seq data analysis of an unlimited number of samples, thus increasing throughput, reproducibility and saving time. Starting from short read sequences, FC performs the following steps: 1) quality controls, 2) alignment to a reference genome, 3) peak calling, 4) genomic annotation, 5) generation of raw signal tracks for visualization on the UCSC genome browser.
FC exploits the fastest and most effective tools today available. Installion on a Mac platform require very basic computational skills while configuration and usage are supported by a user-friendly graphic user interface (GUI). Alternatively, FC can be compiled from the source code on any Unix machine and then run with the possibility of customizing each single parameter through a simple configuration text file that can be generated using a dedicated user-friendly web-form. Considering the performances, FC can be run on a desktop machine, even though the use of a computer cluster is recommended for analyses of large batches of data. FC is perfectly suited to work with data coming from Illumina Solexa Genome Analyzers or ABI SOLiD and its usage can potentially be extended to any sequencing platform. FC is designed for a very broad range of users. While it can be installed and run by wet biologists on a Mac machine, computational biologists can increase reproducibility of their ChIP-seq data analyses while saving time for downstream analyses.
[Please cite Biol Direct. 2011 Oct 6;6(1):51]