Bioassay OntologyVance's Blog

Tag Archive for 'RNAseq'

RNA-seq – not for the faint of heart

Jessica and Dario have been leading our efforts to analyze data from different deep sequencing projects in the lab.  This has been much more challenging than I imagined and I thought it was going to be difficult!  After many months Arpit Mehta, in the HIHG and Frank Kuo, a UM medical student, solved our pipeline problems.  It is pretty alarming to me that it takes days of supercomputer time to run a basic analysis using TopHat, Bowtie and Cufflinks from the UC Berkley Center for Bioinformatics and Computational Biology.  The most interesting things have been the many novel or unexpected alternatively spliced forms of genes expressed in neurons.  It looks like this will turn upside down dogma about many signaling pathways.  Time to get to work with the VTI again.


We are using “Pegasus”, a new Linux-based supercomputer that belongs to the Center for Computational Science to do RNAseq analysis.  Pegasus has 5,000 CPUs and lives at the Terremark Network Access Point (NAP) of the Americas in downtown Miami.  The NAP has a ten gigabit HPC network connection to the UM campuses.  The RNseq analysis is slow – typically taking 12 hours per sample on Pegasus – kind of scary.