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These alignment scripts should always be run with a wayness of 4 (-w 4) in the ls6 batch system, meaning at most 4 commands per node. |
Exercise #4: Bowtie2
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alignment - Vibrio cholerae RNA-seq
While we have focused on aligning eukaryotic data, the same tools can be used with prokaryotic data. The major differences are less about the underlying data and much more about the external/public databases that store and distribute reference data. If we want to study a prokaryote, the reference data is usually downloaded from a resource like GenBank.
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