This pipeline runs sylamer on input fasta file for a list of given miRNA seeds.
files :file:``pipeline.yml and :file:
conf.py`.
See :ref:PipelineSettingUp
and :ref:PipelineRunning
on general
information how to use CGAT pipelines.
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
- 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
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
- directories for each seed before running sylamer on each
- output directories with sylamer results for each miRNA seed present in input list of seeds