sage.rst

Sage

Introduction

Sage is a proteomics search engine - a tool that transforms raw mass spectra from proteomics experiments into peptide identificatons via database searching & spectral matching. But, it's also more than just a search engine - Sage includes a variety of advanced features that make it a one-stop shop: retention time prediction, quantification (both isobaric & LFQ), peptide-spectrum match rescoring, and FDR control.

For more information, please check:

GitHub Packages: https://github.com/lazear/sage/pkgs/container/sage

Home page: https://github.com/lazear/sage

Versions

• 0.8.1

Commands

• sage

Module

You can load the modules by:

module load biocontainers
module load sage

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run sage on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sage
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers sage