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Overview

This pipeline runs sylamer on input fasta file for a list of given miRNA seeds.

files :file:``pipeline.yml and :file:conf.py`.

Usage

See :ref:PipelineSettingUp and :ref:PipelineRunning on general information how to use CGAT pipelines.

Configuration

The pipeline requires a configured :file:pipeline.yml file. CGATReport report requires a :file:conf.py and optionally a :file:cgatreport.ini file (see :ref:PipelineReporting).

Default configuration files can be generated by executing:

python /pipeline_sylamer.py config

Input files

  • fasta file of 3'UTRs of mRNAs to look for miRNA seeds
  • list of miRNA seeds to look for
  • ranked list for each mRNA present in the fasta file

Requirements

On top of the default CGAT setup, the pipeline requires the following software to be installed and in the path: - GSL library and sylamer

/!\Sylamer needs GSL to run On stanage: module load GSL/2.7-GCC-12.2.0

Pipeline output

  • directories for each seed before running sylamer on each
  • output directories with sylamer results for each miRNA seed present in input list of seeds