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CookBook
helios edited this page Oct 25, 2012
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If you followed TopHat in a glance your RNS-Seq data are ready to be cook aka quantified by biongs. As always the software assumes that you respect a precise directory tree structure.
biongs rna:smart_quant gtf Th2 ALL -p 6 --date --grid=parallel
Because we implemented a way to explore the file system and discover projects, samples, and output created by supported programs we can easily process all the samples that are referring to a project. Quantification is a process that can be performed on many samples at the same time, due the fact the datasets are independent. Biongs supports only Parallel for this task but we are working hard to support Slurm and PBS.