RNA-Seq pipeline used at the Delft Bioinformatics Lab for paired and single end reads.

• IBIDAS: https://github.com/mhulsman/ibidas
• Trimmomatic: http://www.usadellab.org/cms/?page=trimmomatic
• STAR: https://code.google.com/p/rna-star/
• SAMTOOLS: http://samtools.sourceforge.net/
• CUFFLINKS: http://cufflinks.cbcb.umd.edu/

Further functionality is provided by installing:

• TRINTITY: http://trinityrnaseq.sourceforge.net/
• BLAST+: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
• HTSeq: http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
• FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
• Matplotlib: http://matplotlib.org/
• LATEX: http://www.latex-project.org/

Given a configuration file (such as 'pipeline_conf_example.py') (most functionality is exemplified there)

> ./pipeline_conf_example.py # Produces a makefile 'Makefile', and a configuration file 'conf'

You can get a status of each step by issuing:

> make status

And you can run any one of these steps with:

> make TRIMMOMATIC

If you start a step and you have not completed the dependencies of that step, it will run those first.

Clone the delftrnaseq repository to somewhere:

> git clone https://github.com/thiesgehrmann/delftrnaseq.git

In each configuration file you create, the first line should reflect the location of 'pipeline.py' in your current installation.