title: Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data.
abstract: BACKGROUND
  High-throughput sequencing is generating massive amounts of data at a pace that largely exceeds the throughput of data analysis routines. Here we introduce Fish the ChIPs (FC), a 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.
  
  
  RESULTS
  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 and IGV genome browsers. FC exploits some of the fastest and most effective tools today available. Installation on a Mac platform requires very basic computational skills while configuration and usage are supported by a user-friendly graphic user interface. 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 execution time, 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.
  
  
  CONCLUSIONS
  Compared to existing tools, FC has two main advantages that make it suitable for a broad range of users. First of all, it can be installed and run by wet biologists on a Mac machine. Besides it can handle an unlimited number of samples, being convenient for large analyses. In this context, computational biologists can increase reproducibility of their ChIP-Seq data analyses while saving time for downstream analyses.
authors: Department of Experimental Oncology, European Institute of Oncology (IEO), IFOM-IEO Campus, Via Adamello 16, Milan, Italy. iros.barozzi@gmail.com
authors: Iros
authors: I
authors: Barozzi
authors: Alberto
authors: A
authors: Termanini
authors: Saverio
authors: S
authors: Minucci
authors: Gioacchino
authors: G
authors: Natoli
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D003196:Computer Graphics; D030541:Databases, Genetic; D016678:Genome; D020407:Internet; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D015203:Reproducibility of Results; D016415:Sequence Alignment; D012984:Software; D013997:Time Factors