Tuesday, 19th October, 2010, 11:00

Analyzing Chip-Seq mapped reads with Pyicos and bash: Command-line real time examples.

When provided with some files with mapped reads coming from a Chip-Seq experiment, lots of the work has already been done. Extracting the biological information from them should be an easy job, right? Surprisingly, lots of bioinformaticians are finding that the methods and software packages proposed for the analysis of this kind of data doesn’t fit their particular needs. Because these experiments have gone through a long process and they commonly targets a particular Protein-DNA interactions, this last step normally takes longer than expected. Moreover, the technical difficulties of dealing with read files that can be on the Gigabyte-Scale, the different formats used by different laboratories and tools and the novelty of the field are extra headaches for the researcher performing this kind of analysis. This seminar is designed as an introduction where I will work in real-time with a sample dataset, showing how to use bash and Pyicos, a novel toolbox for the analysis of mapped reads coming from Deep Sequencing experiments.

Speaker: Juan Gonzalez-Vallinas-Regulatory Genomics Group, GRIB

Room PRBB room 173.06-183.01 (Xipre)