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NAME

lincRNA_pipeline

DESCRIPTION

This document describes a pipeline that integrates several Python script and linux commands to generate long non-coding RNA (lncRNA) from TopHat-Cufflinks-Cuffcompare output

USUAGE NOTES

The pipeline can be run by using the script lincRNA_pipeline.sh

./lincRNA_pipeline.sh

          	-c    /path/to/cuffcompare_output file
            -g    /path/to/reference genome file
            -r    /path/to/reference CDS file
            -b    /path/to/RNA file

EXAMPLE

./lincRNA_pipeline.sh -c cuffcompare_out_annot_no_annot.combined.gtf -g Brapa_sequence_v1.2_genome.fa -r Brassica_rapa_v1.2_cds.fa -b TE_RNA_transcripts.fa