Salmon

Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the novel concept of lightweight alignment with a streaming inference algorithm) to provide accurate expression estimates very quickly (i.e.wicked-fast) and while using very little memory. Salmon performs its inference using an expressive and realistic model of RNA-seq data that takes into account the attributes, like position-specfic bias, observed in real experimental data.

 

Documentation

 

Usage

  • Bridges

To see what other modules are needed, what commands are available and how to get additional help type

module help salmon

To see what versions of Salmon are available type

module avail salmon

To use Salmon, include a command like this in your batch script to load the Salmon module:

module load salmon

Be sure you also load any other modules needed, as listed by the module help salmon command.

User Information

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Send mail to remarks@psc.edu or call the PSC hotline: 412-268-6350.