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Tutorial for running FLAMES on Esrum

FLAMES is a gene prioritization method that predicts the most likely effector gene in a locus. You can find the official Github here, and the publication here.

FLAMES has been made available as an environment module in the loos_group-AUDIT folder on Esrum. This tutorial describes how you can load FLAMES and run it in a script. You can find the tutorial scripts at /projects/loos_group-AUDIT/data/tutorials/flames_tutorial/.

FLAMES method builds on the result files from PoPS and MAGMA, so please refer to those tutorials before your run FLAMES. You will need the following files-

  1. From MAGMA:
    • .genes.annot file from MAGMA annotation step
    • .genes.out file from MAGMA gene analysis step
    • .genes.raw file from MAGMA gene analysis step
    • .gsa.out file from MAGMA gene level analysis step
  2. From PoPS:
    • .preds file with the PoPS scores from the final PoPS step